1hfe

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Method: X-RAY DIFFRACTION D_max: 106.9 Å Quality: GOOD

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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))

OrganismNot specified

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 S； UniProt 1–123	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 1 （P07598） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain T； UniProt 1–123	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 1 （P07598） 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain S； UniProt 1–123 Chain T； UniProt 1–123	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 2 （P07598） 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

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 1HFE	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
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 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 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 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 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 construct 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 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 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 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 construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 27 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 S； PDBConstruct 1–123； UniProt 1–123 Author chain T； PDBConstruct 1–123； UniProt 1–123

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))

OrganismNot specified

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 L； UniProt 1–421	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 1 （P07603） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 1–421	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 1 （P07603） 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain L； UniProt 1–421 Chain M； UniProt 1–421	Not recorded	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 2 （P07603） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1HFE	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
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 construct 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 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 construct 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 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 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 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 construct 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 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 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 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 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 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 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 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 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 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 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHFL_DESVH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–421； UniProt 1–421 Author chain M； PDBConstruct 1–421； UniProt 1–421

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hfe
Deposition date deposition_date	1998-11-11
Structure title title	1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
Keywords keywords	FE-ONLY HYDROGENASE, HYDROGENE METABOLISM, PERIPLASM, HYDROGENASE; HYDROGENASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	33.14 Å
Radius of gyration Rg (electron density) rg_electron	32.60 Å
Forward intensity I(0) i0	197212000.00
Molecular weight molecular_weight	109530.0 kDa
Excluded volume excluded_volume	135340 Å³
Envelope volume envelope_volume	161380 Å³
Hydration-shell volume shell_volume	41184 Å³
Envelope diameter envelope_diameter	110.1 Å
Shell Rg shell_rg	39.54 Å
Envelope Rg envelope_rg	32.59 Å
Shape Rg shape_rg	32.56 Å
Total Rg total_rg	33.22 Å
Total atoms total_atoms	7549
Residues n_residues	970
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

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

Maximum dimension Dmax dmax	106.9 Å
Rg (real space) rg_real	33.27 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.9720e+08
I(0) uncertainty (real space) i0_real_error	3.4370e+06
Rg (reciprocal space) rg_reciprocal	33.22 Å
I(0) (reciprocal space) i0_reciprocal	197200000.0000
Solution quality estimate total_estimate	0.8732
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.693
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	135800000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.888

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
Molecular weight formula_weight	13646.8 kDa
EC 编号 ec_number	1.18.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T
Atom count atom_count	9079

MQIASITRRGFLKVACVTTGAALIGIRMTGKAVAAVKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Entity 2 Entity 2 polymer

Description description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
Molecular weight formula_weight	46011.1 kDa
EC 编号 ec_number	1.18.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAMDRTTTRLYAGLKKRLAMASANKA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	1,3-PROPANEDITHIOL
Molecular weight formula_weight	108.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	CYSTEINE
Molecular weight formula_weight	121.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1179

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1hfel1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d1hfel2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d1hfem1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d1hfem2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d1hfes_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
Family Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

Domain ID domain_id	d1hfet_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
Family Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

CATH v4.4 (8 domains)

Domain ID domain_id	1hfeL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1780 —

Domain ID domain_id	1hfeL02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1hfeL03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homologous superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

Domain ID domain_id	1hfeM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1780 —

Domain ID domain_id	1hfeM02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1hfeM03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homologous superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

Domain ID domain_id	1hfeS00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

Domain ID domain_id	1hfeT00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

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8. Citations (1)

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Unit-cell length a length_a	128.970 Å
Unit-cell length b length_b	123.070 Å
Unit-cell length c length_c	65.070 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	—
R_work r_work	0.1582
R_free r_free	0.1820

fit	/app/data/saxs_computation/hf/1hfe/1hfe.fit
pddf	/app/data/pr_computation/hf/1hfe/1hfe.pr.out
profile	/app/data/saxs_computation/hf/1hfe/1hfe.dat

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER 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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)