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8ru6

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum

Method: X-RAY DIFFRACTION Dmax: 67.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit

Nitratidesulfovibrio vulgaris

UniProt P07598

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–392 Not recorded PG4 TETRAETHYLENE GLYCOL × 4 SF4 IRON/SULFUR CLUSTER × 3 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000 Resolution 1.15 Å R-free 0.158

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8RU6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GX7 Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase Deposited 2002-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 27–397（371 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared
NMR measurement conditions pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1
Resolution not provided
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–421（421 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–421（421 aa）
Not recorded FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–421（421 aa）
Chain M 1–421（421 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 4 CYN CYANIDE ION × 4 SF4 IRON/SULFUR CLUSTER × 6 PDT 1,3-PROPANEDITHIOL × 2 CMO CARBON MONOXIDE × 4 CYS CYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
8BJ7 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Hinact-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；281.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.04 Å R-free 0.167
8BJ8 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Htrans-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；295.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.01 Å R-free 0.163
8RTG Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase in apo form Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 27.5 % Polyethylene glycol 4000
Resolution 1.46 Å R-free 0.189
8RTI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form derivatized with krypton Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.50 Å R-free 0.194
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 LFH dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000
Resolution 1.48 Å R-free 0.181
8RXJ Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 10 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 CYN CYANIDE ION × 1 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.51 Å R-free 0.186
8RYH Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica Deposited 2024-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–389（389 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.77 Å R-free 0.246
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–389（389 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–389（389 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GNK Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded CMO CARBON MONOXIDE × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 6 PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500
Resolution 1.05 Å R-free 0.185
9GZ0 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - oxidised state Deposited 2024-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% PEG 6000
Resolution 1.02 Å R-free 0.166
9GZ4 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state Deposited 2024-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 0.96 Å R-free 0.152
9GZL Apo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine Deposited 2024-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 CL CHLORIDE ION × 7 LI LITHIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 1.02 Å R-free 0.153
9HPX [FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand. Deposited 2024-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 A1IW2 6,6,7,7-tetrakis($l^{3}-oxidanylidynemethyl)-1$l^{3},5$l^{3}-dithia-3-aza-6$l^{5},7$l^{4}-diferrabicyclo[3.1.1]heptane-6-carbonitrile × 1 CL CHLORIDE ION × 10 LI LITHIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiCl 0.1 M Sodium Acetate 26-32% PEG 6000
Resolution 0.96 Å R-free 0.144
9QD6 High resolution structure of the artificially maturated [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.18 Å R-free 0.169
9QDC Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；35% (w/v) PEG 4000, 1M LiCl, 0.1M sodium formate pH 4.6
Resolution 1.49 Å R-free 0.181
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate pH 5.3
Resolution 1.20 Å R-free 0.220
9QDG Nitratidesulfovibrio vulgaris [FeFe] hydrogenase crystallized in the sodium propionate buffer at pH 5.0 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium propionate pH 5.0
Resolution 1.02 Å R-free 0.207
9QIS CO-bound [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 CMO CARBON MONOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；37% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.49 Å R-free 0.176
9R9Q [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.04 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.62 Å R-free 0.197
9R9R [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.21 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.58 Å R-free 0.202
9R9S [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.71 Å R-free 0.174
9R9T [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.81 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å R-free 0.242
9R9U [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 6.62 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.31 Å R-free 0.162
9R9V [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 7.00 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–395（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.25 Å R-free 0.153

26 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHFL_DESVH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–392； UniProt 1–392

Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit

Nitratidesulfovibrio vulgaris

UniProt P07603

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 39–123 Not recorded PG4 TETRAETHYLENE GLYCOL × 4 SF4 IRON/SULFUR CLUSTER × 3 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000 Resolution 1.15 Å R-free 0.158

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8RU6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GX7 Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase Deposited 2002-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared
NMR measurement conditions pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1
Resolution not provided
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 1–123（123 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–123（123 aa）
Not recorded FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–123（123 aa）
Chain T 1–123（123 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 4 CYN CYANIDE ION × 4 SF4 IRON/SULFUR CLUSTER × 6 PDT 1,3-PROPANEDITHIOL × 2 CMO CARBON MONOXIDE × 4 CYS CYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
8BJ7 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Hinact-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；281.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.04 Å R-free 0.167
8BJ8 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Htrans-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；295.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.01 Å R-free 0.163
8RTG Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase in apo form Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 27.5 % Polyethylene glycol 4000
Resolution 1.46 Å R-free 0.189
8RTI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form derivatized with krypton Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.50 Å R-free 0.194
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 LFH dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000
Resolution 1.48 Å R-free 0.181
8RXJ Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 10 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 CYN CYANIDE ION × 1 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.51 Å R-free 0.186
8RYH Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica Deposited 2024-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–123（78 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.77 Å R-free 0.246
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–123（78 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 46–123（78 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GNK Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 45–123（79 aa）
Not recorded CMO CARBON MONOXIDE × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 6 PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500
Resolution 1.05 Å R-free 0.185
9GZ0 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - oxidised state Deposited 2024-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% PEG 6000
Resolution 1.02 Å R-free 0.166
9GZ4 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state Deposited 2024-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 0.96 Å R-free 0.152
9GZL Apo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine Deposited 2024-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 CL CHLORIDE ION × 7 LI LITHIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 1.02 Å R-free 0.153
9HPX [FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand. Deposited 2024-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 A1IW2 6,6,7,7-tetrakis($l^{3}-oxidanylidynemethyl)-1$l^{3},5$l^{3}-dithia-3-aza-6$l^{5},7$l^{4}-diferrabicyclo[3.1.1]heptane-6-carbonitrile × 1 CL CHLORIDE ION × 10 LI LITHIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiCl 0.1 M Sodium Acetate 26-32% PEG 6000
Resolution 0.96 Å R-free 0.144
9QD6 High resolution structure of the artificially maturated [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.18 Å R-free 0.169
9QDC Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；35% (w/v) PEG 4000, 1M LiCl, 0.1M sodium formate pH 4.6
Resolution 1.49 Å R-free 0.181
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate pH 5.3
Resolution 1.20 Å R-free 0.220
9QDG Nitratidesulfovibrio vulgaris [FeFe] hydrogenase crystallized in the sodium propionate buffer at pH 5.0 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium propionate pH 5.0
Resolution 1.02 Å R-free 0.207
9QIS CO-bound [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 CMO CARBON MONOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；37% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.49 Å R-free 0.176
9R9Q [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.04 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.62 Å R-free 0.197
9R9R [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.21 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.58 Å R-free 0.202
9R9S [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.71 Å R-free 0.174
9R9T [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.81 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å R-free 0.242
9R9U [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 6.62 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.31 Å R-free 0.162
9R9V [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 7.00 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.25 Å R-free 0.153

26 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHFS_DESVH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 397–481； UniProt 39–123

Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit

Nitratidesulfovibrio vulgaris

UniProt P29166

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 515–518 Not recorded PG4 TETRAETHYLENE GLYCOL × 4 SF4 IRON/SULFUR CLUSTER × 3 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000 Resolution 1.15 Å R-free 0.158

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8RU6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C4A BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM Deposited 1999-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC1 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.40 Å R-free 0.254
1C4C BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM Deposited 1999-08-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC0 2 IRON/2 SULFUR/6 CARBONYL/1 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.40 Å R-free 0.240
1FEH FE-ONLY HYDROGENASE FROM CLOSTRIDIUM PASTEURIANUM Deposited 1998-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC1 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.1；25% PEG4000, 0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM SULFATE, pH 5.1
Resolution 1.80 Å R-free 0.235
3C8Y 1.39 Angstrom crystal structure of Fe-only hydrogenase Deposited 2008-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HCN 2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHER CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions capillary diffusion；pH 4.6；298 K；25% PEG 4000, 0.1M Sodium acetate (pH 4.6),0.1M Sodium sulfate, capillary diffusion, temperature 298K
Resolution 1.39 Å R-free 0.194
4XDC Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor Deposited 2014-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG3000, MgCl
Resolution 1.63 Å R-free 0.176
4XDC Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor Deposited 2014-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG3000, MgCl
Resolution 1.63 Å R-free 0.176
4XDD Apo [FeFe]-Hydrogenase CpI Deposited 2014-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 MG MAGNESIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG4000, MgCl
Resolution 1.60 Å R-free 0.166
4XDD Apo [FeFe]-Hydrogenase CpI Deposited 2014-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 MG MAGNESIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG4000, MgCl
Resolution 1.60 Å R-free 0.166
5BYQ Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WV bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；19% PEG 4000, 0.4 M MgCl,0.1 M MES, 21 % glycerol
Resolution 1.73 Å R-free 0.176
5BYQ Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WV bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；19% PEG 4000, 0.4 M MgCl,0.1 M MES, 21 % glycerol
Resolution 1.73 Å R-free 0.176
5BYR Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 4000, 0.4 M MgCl,0.1 M MES, 25 % glycerol
Resolution 1.82 Å R-free 0.192
5BYR Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 4000, 0.4 M MgCl,0.1 M MES, 25 % glycerol
Resolution 1.82 Å R-free 0.192
5BYS Semisynthetic [FeFe]-hydrogenase CpI with sulfur-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WX bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(sulfanediyldimethanethiolatato-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl,0.1 M MES, 19 % glycerol
Resolution 1.93 Å R-free 0.188
5BYS Semisynthetic [FeFe]-hydrogenase CpI with sulfur-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WX bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(sulfanediyldimethanethiolatato-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl,0.1 M MES, 19 % glycerol
Resolution 1.93 Å R-free 0.188
5LA3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A Deposited 2016-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E279A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 4000, 0.4 M MgCl2,0.1 M MES, 16 % glycerol
Resolution 2.29 Å R-free 0.213
5LA3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A Deposited 2016-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E279A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 4000, 0.4 M MgCl2,0.1 M MES, 16 % glycerol
Resolution 2.29 Å R-free 0.213
5OEF Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor Deposited 2017-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 9SQ dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM MES pH 6.5, 0.2 M MgCl2 19 % PEG 4000 21 % Glycerol
Resolution 2.05 Å R-free 0.269
5OEF Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor Deposited 2017-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 9SQ dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM MES pH 6.5, 0.2 M MgCl2 19 % PEG 4000 21 % Glycerol
Resolution 2.05 Å R-free 0.269
6GLY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：C299A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.09 Å R-free 0.209
6GLY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：C299A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.09 Å R-free 0.209
6GLZ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Mutation：C299D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.02 Å R-free 0.249
6GLZ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Mutation：C299D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.02 Å R-free 0.249
6GM0 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E279Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 2.11 Å R-free 0.228
6GM0 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E279Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 2.11 Å R-free 0.228
6GM1 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E282A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.05 Å R-free 0.205
6GM1 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E282A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.05 Å R-free 0.205
6GM2 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Mutation：E282D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.76 Å R-free 0.276
6GM2 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Mutation：E282D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.76 Å R-free 0.276
6GM3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant R286A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：R286A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；23% PEG 4000, 0.4 M MgCl2,0.1 M MES, 17 % glycerol
Resolution 2.22 Å R-free 0.230
6GM3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant R286A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：R286A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；23% PEG 4000, 0.4 M MgCl2,0.1 M MES, 17 % glycerol
Resolution 2.22 Å R-free 0.230
6GM4 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S319A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：S319A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 1.97 Å R-free 0.202
6GM4 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S319A Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：S319A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 1.97 Å R-free 0.202
6GM8 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E282Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.96 Å R-free 0.221
6GM8 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q Deposited 2018-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E282Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.96 Å R-free 0.221
6H63 Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor Deposited 2018-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded FU8 dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；22% PEG 4000, 0.4 M MgCl2,0.1 M MES, 18 % glycerol
Resolution 2.08 Å R-free 0.245
6H63 Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor Deposited 2018-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded FU8 dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；22% PEG 4000, 0.4 M MgCl2,0.1 M MES, 18 % glycerol
Resolution 2.08 Å R-free 0.245
6N59 1.0 Angstrom crystal structure of [FeFe]-hydrogenase Deposited 2018-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 4.6；298 K；25% PEG 4000, 0.1 M Sodium acetate (pH 4.6), 0.1 M Sodium sulfate, 1 mM Sodium Dithionite
Resolution 1.02 Å R-free 0.132
6N6P Crystal structure of [FeFe]-hydrogenase in the presence of 7 mM Sodium dithionite Deposited 2018-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；298 K；25% PEG 4000, 0.1 M Sodium acetate (pH 4.6), 0.1 M Sodium sulfate, capillary diffusion. Crystals were treated with 7 mM Sodium sulfite prior freezing
Resolution 1.95 Å R-free 0.204
6NAC Crystal structure of [FeFe]-hydrogenase I (CpI) solved with single pulse free electron laser data Deposited 2018-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 4.6；298 K；25% PEG 4000, 0.1M Sodium acetate (pH 4.6), 0.1M Sodium sulfate,
Resolution 1.55 Å R-free 0.285
6YF4 [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant E279D Deposited 2020-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Mutation：E279D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6), 20%PEG4000, 20% Glycerol, 0.4M MgCl2
Resolution 1.77 Å R-free 0.234
6YF4 [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant E279D Deposited 2020-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Mutation：E279D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6), 20%PEG4000, 20% Glycerol, 0.4M MgCl2
Resolution 1.77 Å R-free 0.234
7QHF [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant G302S Deposited 2021-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes-NaOH (pH 6.0), 0.4 M MgCl2, 20% PEG4000, 20% glycerol
Resolution 1.63 Å R-free 0.192
7QHF [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant G302S Deposited 2021-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes-NaOH (pH 6.0), 0.4 M MgCl2, 20% PEG4000, 20% glycerol
Resolution 1.63 Å R-free 0.192
8AIO CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH(pH6.0), 0.4M MgCl2, 19%PEG4000, 21%glycerol
Resolution 1.52 Å R-free 0.192
8AIO CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH(pH6.0), 0.4M MgCl2, 19%PEG4000, 21%glycerol
Resolution 1.52 Å R-free 0.192
8AJ6 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH pH6.0, 21% PEG; 19% Glycerol; 0.4M MgCl2;
Resolution 1.50 Å R-free 0.199
8AJ6 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH pH6.0, 21% PEG; 19% Glycerol; 0.4M MgCl2;
Resolution 1.50 Å R-free 0.199
8ALN CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.34 Angstrom Deposited 2022-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 0.4M MgCl2, 19% PEG4000, 21% glycerol
Resolution 1.34 Å R-free 0.175
8ALN CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.34 Angstrom Deposited 2022-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 0.4M MgCl2, 19% PEG4000, 21% glycerol
Resolution 1.34 Å R-free 0.175
8AP2 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.39 Angstrom Deposited 2022-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 4 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 19% PEG4000, 21% glycerol, 0.4M MgCl2
Resolution 1.39 Å R-free 0.191
8AP2 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.39 Angstrom Deposited 2022-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 19% PEG4000, 21% glycerol, 0.4M MgCl2
Resolution 1.39 Å R-free 0.191
8CJY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T Deposited 2023-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes pH6.0, 20% PEG4000, 20% glycerol, 0.4M MgCl2
Resolution 1.60 Å R-free 0.187
8CJY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T Deposited 2023-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes pH6.0, 20% PEG4000, 20% glycerol, 0.4M MgCl2
Resolution 1.60 Å R-free 0.187
8PVM formaldehyde-inhibited [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2023-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–574（574 aa）
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 8 FES FE2/S2 (INORGANIC) CLUSTER × 2 74C methyl radical × 3 GOL GLYCEROL × 4 FOR FORMYL GROUP × 2 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes (pH6.0), 0.4 M MgCl2, 20 % PEG4000, 20% glycerol
Resolution 1.38 Å R-free 0.175
8QM3 formaldehyde-inhibited [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 8 FES FE2/S2 (INORGANIC) CLUSTER × 2 FOR FORMYL GROUP × 10 GOL GLYCEROL × 4 CL CHLORIDE ION × 7 MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH 6), 0.4M MgCl2, 20% PEG4000, 20% glyerol
Resolution 1.53 Å R-free 0.194
9RJ9 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.45 Å R-free 0.191
9RJ9 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.45 Å R-free 0.191
9RJO [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.67 Å R-free 0.206
9RJO [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.67 Å R-free 0.206
9RJQ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.75 Å R-free 0.220
9RJQ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L Deposited 2025-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.75 Å R-free 0.220

35 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHF1_CLOPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 393–396； UniProt 515–518

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8ru6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ru6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ru6
Deposition date deposition_date2024-01-30
Structure title titleNitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum
Keywords keywords[FeFe] hydrogenase, iron-sulfur cluster, metalloenzyme, hydrogen production, fusion protein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.95 Å
Radius of gyration Rg (electron density) rg_electron21.12 Å
Forward intensity I(0) i053194300.00
Molecular weight molecular_weight55403.0 kDa
Excluded volume excluded_volume68511 ų
Envelope volume envelope_volume76569 ų
Hydration-shell volume shell_volume28528 ų
Envelope diameter envelope_diameter70.7 Å
Shell Rg shell_rg29.47 Å
Envelope Rg envelope_rg21.67 Å
Shape Rg shape_rg21.19 Å
Total Rg total_rg21.83 Å
Total atoms total_atoms7577
Residues n_residues484
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.4 Å
Rg (real space) rg_real21.80 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real5.3190e+07
I(0) uncertainty (real space) i0_real_error7.2640e+05
Rg (reciprocal space) rg_reciprocal21.83 Å
I(0) (reciprocal space) i0_reciprocal53200000.0000
Solution quality estimate total_estimate0.8231
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2 Å
Skewness Skewness skewness0.177
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17810000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)