9qdc

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6

Method: X-RAY DIFFRACTION D_max: 67.2 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic [Fe] hydrogenase small subunit

Nitratidesulfovibrio vulgaris str. Hildenborough

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 36–123	Not recorded	Periplasmic [Fe] hydrogenase large subunit × 1 （P07598） 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

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 9QDC	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 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 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 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 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 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 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 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
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 Deposited 2024-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–123（85 aa）	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
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07	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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06	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 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 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 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 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 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 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 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 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_NITV2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–88； UniProt 36–123

Periplasmic [Fe] hydrogenase large subunit

Nitratidesulfovibrio vulgaris str. Hildenborough

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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–397	Not recorded	Periplasmic [Fe] hydrogenase small subunit × 1 （P07603） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9QDC	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 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 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 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 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 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 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
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 Deposited 2024-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–392（392 aa）	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
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07	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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06	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 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 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 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 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 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 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 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 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_NITV2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–397； UniProt 1–397

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9qdc
Deposition date deposition_date	2025-03-06
最后修订 last_revision	2026-03-18
Structure title title	Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6
Keywords keywords	[FeFe] hydrogenase, iron-sulfur cluster, metalloenzyme, hydrogen production, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.66 Å
Radius of gyration Rg (electron density) rg_electron	20.86 Å
Forward intensity I(0) i0	51105800.00
Molecular weight molecular_weight	54339.0 kDa
Excluded volume excluded_volume	67190 Å³
Envelope volume envelope_volume	73465 Å³
Hydration-shell volume shell_volume	27823 Å³
Envelope diameter envelope_diameter	70.9 Å
Shell Rg shell_rg	28.98 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	20.92 Å
Total Rg total_rg	21.53 Å
Total atoms total_atoms	7435
Residues n_residues	481
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.2 Å
Rg (real space) rg_real	21.51 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	5.1110e+07
I(0) uncertainty (real space) i0_real_error	6.1640e+05
Rg (reciprocal space) rg_reciprocal	21.54 Å
I(0) (reciprocal space) i0_reciprocal	51110000.0000
Solution quality estimate total_estimate	0.8960
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17010000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.952

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Periplasmic [Fe] hydrogenase small subunit
Molecular weight formula_weight	10082.4 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	8075

VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

来源 Source

来源生物 organism	Nitratidesulfovibrio vulgaris str. Hildenborough
NCBI Class编号 ncbi_taxonomy_id	882
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Periplasmic [Fe] hydrogenase large subunit
Molecular weight formula_weight	44397.1 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAWSHPQFEK

来源 Source

来源生物 organism	Nitratidesulfovibrio vulgaris str. Hildenborough
NCBI Class编号 ncbi_taxonomy_id	882
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
Molecular weight formula_weight	355.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	410

▶

8. Citations (1)

▶

Unit-cell length a length_a	49.535 Å
Unit-cell length b length_b	87.568 Å
Unit-cell length c length_c	89.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.491 Å
Low-resolution limit resolution_low	44.640 Å
R factor r_factor	—
R_work r_work	0.1473
R_free r_free	0.1815

fit	/app/data/saxs_computation/qd/9qdc/9qdc.fit
pddf	/app/data/pr_computation/qd/9qdc/9qdc.pr.out
profile	/app/data/saxs_computation/qd/9qdc/9qdc.dat

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6

1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic [Fe] hydrogenase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Periplasmic [Fe] hydrogenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)