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3c8y

1.39 Angstrom crystal structure of Fe-only hydrogenase

Method: X-RAY DIFFRACTION Dmax: 83.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Iron hydrogenase 1

OrganismNot specified

UniProt P29166

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–574 Not recorded HCN 2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHER CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：capillary diffusion；pH 4.6；298 K；25% PEG 4000, 0.1M Sodium acetate (pH 4.6),0.1M Sodium sulfate, capillary diffusion, temperature 298K Resolution 1.39 Å R-free 0.194

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 3C8Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C4A BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM Deposited 1999-08-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC1 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.40 Å R-free 0.254
1C4C BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM Deposited 1999-08-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC0 2 IRON/2 SULFUR/6 CARBONYL/1 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.40 Å R-free 0.240
1FEH FE-ONLY HYDROGENASE FROM CLOSTRIDIUM PASTEURIANUM Deposited 1998-10-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded HC1 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.1；25% PEG4000, 0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM SULFATE, pH 5.1
Resolution 1.80 Å R-free 0.235
4XDC Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor Deposited 2014-12-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG3000, MgCl
Resolution 1.63 Å R-free 0.176
4XDC Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor Deposited 2014-12-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；PEG3000, MgCl
Resolution 1.63 Å R-free 0.176
4XDD Apo [FeFe]-Hydrogenase CpI Deposited 2014-12-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 MG MAGNESIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG4000, MgCl
Resolution 1.60 Å R-free 0.166
4XDD Apo [FeFe]-Hydrogenase CpI Deposited 2014-12-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 MG MAGNESIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG4000, MgCl
Resolution 1.60 Å R-free 0.166
5BYQ Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WV bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；19% PEG 4000, 0.4 M MgCl,0.1 M MES, 21 % glycerol
Resolution 1.73 Å R-free 0.176
5BYQ Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WV bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；19% PEG 4000, 0.4 M MgCl,0.1 M MES, 21 % glycerol
Resolution 1.73 Å R-free 0.176
5BYR Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 4000, 0.4 M MgCl,0.1 M MES, 25 % glycerol
Resolution 1.82 Å R-free 0.192
5BYR Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 4000, 0.4 M MgCl,0.1 M MES, 25 % glycerol
Resolution 1.82 Å R-free 0.192
5BYS Semisynthetic [FeFe]-hydrogenase CpI with sulfur-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WX bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(sulfanediyldimethanethiolatato-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl,0.1 M MES, 19 % glycerol
Resolution 1.93 Å R-free 0.188
5BYS Semisynthetic [FeFe]-hydrogenase CpI with sulfur-dithiolato-bridged [2Fe] cofactor Deposited 2015-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 1–574（574 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 4WX bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(sulfanediyldimethanethiolatato-1kappaS:2kappaS)diiron(2+) × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl,0.1 M MES, 19 % glycerol
Resolution 1.93 Å R-free 0.188
5LA3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A Deposited 2016-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E279A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 4000, 0.4 M MgCl2,0.1 M MES, 16 % glycerol
Resolution 2.29 Å R-free 0.213
5LA3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A Deposited 2016-06-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E279A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 4000, 0.4 M MgCl2,0.1 M MES, 16 % glycerol
Resolution 2.29 Å R-free 0.213
5OEF Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor Deposited 2017-07-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 9SQ dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM MES pH 6.5, 0.2 M MgCl2 19 % PEG 4000 21 % Glycerol
Resolution 2.05 Å R-free 0.269
5OEF Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor Deposited 2017-07-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 9SQ dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM MES pH 6.5, 0.2 M MgCl2 19 % PEG 4000 21 % Glycerol
Resolution 2.05 Å R-free 0.269
6GLY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：C299A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.09 Å R-free 0.209
6GLY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：C299A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.09 Å R-free 0.209
6GLZ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Mutation：C299D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.02 Å R-free 0.249
6GLZ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Mutation：C299D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.02 Å R-free 0.249
6GM0 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E279Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 2.11 Å R-free 0.228
6GM0 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279Q Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E279Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 2.11 Å R-free 0.228
6GM1 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E282A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.05 Å R-free 0.205
6GM1 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E282A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.05 Å R-free 0.205
6GM2 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D Deposited 2018-05-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Mutation：E282D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.76 Å R-free 0.276
6GM2 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D Deposited 2018-05-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Mutation：E282D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 2.76 Å R-free 0.276
6GM3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant R286A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：R286A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；23% PEG 4000, 0.4 M MgCl2,0.1 M MES, 17 % glycerol
Resolution 2.22 Å R-free 0.230
6GM3 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant R286A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：R286A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；23% PEG 4000, 0.4 M MgCl2,0.1 M MES, 17 % glycerol
Resolution 2.22 Å R-free 0.230
6GM4 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S319A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa） Fragment：complete enzyme
Mutation：S319A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 1.97 Å R-free 0.202
6GM4 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S319A Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa） Fragment：complete enzyme
Mutation：S319A 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol
Resolution 1.97 Å R-free 0.202
6GM8 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–574（573 aa）
Mutation：E282Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.96 Å R-free 0.221
6GM8 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282Q Deposited 2018-05-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–574（573 aa）
Mutation：E282Q 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.96 Å R-free 0.221
6H63 Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor Deposited 2018-07-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded FU8 dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；22% PEG 4000, 0.4 M MgCl2,0.1 M MES, 18 % glycerol
Resolution 2.08 Å R-free 0.245
6H63 Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor Deposited 2018-07-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded FU8 dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；22% PEG 4000, 0.4 M MgCl2,0.1 M MES, 18 % glycerol
Resolution 2.08 Å R-free 0.245
6N59 1.0 Angstrom crystal structure of [FeFe]-hydrogenase Deposited 2018-11-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 4.6；298 K；25% PEG 4000, 0.1 M Sodium acetate (pH 4.6), 0.1 M Sodium sulfate, 1 mM Sodium Dithionite
Resolution 1.02 Å R-free 0.132
6N6P Crystal structure of [FeFe]-hydrogenase in the presence of 7 mM Sodium dithionite Deposited 2018-11-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；298 K；25% PEG 4000, 0.1 M Sodium acetate (pH 4.6), 0.1 M Sodium sulfate, capillary diffusion. Crystals were treated with 7 mM Sodium sulfite prior freezing
Resolution 1.95 Å R-free 0.204
6NAC Crystal structure of [FeFe]-hydrogenase I (CpI) solved with single pulse free electron laser data Deposited 2018-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 4.6；298 K；25% PEG 4000, 0.1M Sodium acetate (pH 4.6), 0.1M Sodium sulfate,
Resolution 1.55 Å R-free 0.285
6YF4 [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant E279D Deposited 2020-03-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Mutation：E279D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6), 20%PEG4000, 20% Glycerol, 0.4M MgCl2
Resolution 1.77 Å R-free 0.234
6YF4 [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant E279D Deposited 2020-03-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Mutation：E279D 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6), 20%PEG4000, 20% Glycerol, 0.4M MgCl2
Resolution 1.77 Å R-free 0.234
7QHF [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant G302S Deposited 2021-12-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes-NaOH (pH 6.0), 0.4 M MgCl2, 20% PEG4000, 20% glycerol
Resolution 1.63 Å R-free 0.192
7QHF [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant G302S Deposited 2021-12-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes-NaOH (pH 6.0), 0.4 M MgCl2, 20% PEG4000, 20% glycerol
Resolution 1.63 Å R-free 0.192
8AIO CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH(pH6.0), 0.4M MgCl2, 19%PEG4000, 21%glycerol
Resolution 1.52 Å R-free 0.192
8AIO CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH(pH6.0), 0.4M MgCl2, 19%PEG4000, 21%glycerol
Resolution 1.52 Å R-free 0.192
8AJ6 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH pH6.0, 21% PEG; 19% Glycerol; 0.4M MgCl2;
Resolution 1.50 Å R-free 0.199
8AJ6 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2022-07-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH pH6.0, 21% PEG; 19% Glycerol; 0.4M MgCl2;
Resolution 1.50 Å R-free 0.199
8ALN CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.34 Angstrom Deposited 2022-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 0.4M MgCl2, 19% PEG4000, 21% glycerol
Resolution 1.34 Å R-free 0.175
8ALN CO-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.34 Angstrom Deposited 2022-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 0.4M MgCl2, 19% PEG4000, 21% glycerol
Resolution 1.34 Å R-free 0.175
8AP2 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.39 Angstrom Deposited 2022-08-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 4 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 19% PEG4000, 21% glycerol, 0.4M MgCl2
Resolution 1.39 Å R-free 0.191
8AP2 cyanide-bound [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) at 1.39 Angstrom Deposited 2022-08-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH6.0), 19% PEG4000, 21% glycerol, 0.4M MgCl2
Resolution 1.39 Å R-free 0.191
8CJY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T Deposited 2023-02-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes pH6.0, 20% PEG4000, 20% glycerol, 0.4M MgCl2
Resolution 1.60 Å R-free 0.187
8CJY [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant S357T Deposited 2023-02-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；0.1M Mes pH6.0, 20% PEG4000, 20% glycerol, 0.4M MgCl2
Resolution 1.60 Å R-free 0.187
8PVM formaldehyde-inhibited [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D Deposited 2023-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–574（574 aa）
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 8 FES FE2/S2 (INORGANIC) CLUSTER × 2 74C methyl radical × 3 GOL GLYCEROL × 4 FOR FORMYL GROUP × 2 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes (pH6.0), 0.4 M MgCl2, 20 % PEG4000, 20% glycerol
Resolution 1.38 Å R-free 0.175
8QM3 formaldehyde-inhibited [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–574（574 aa） Fragment：complete enzyme
Chain B 1–574（574 aa） Fragment：complete enzyme
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 8 FES FE2/S2 (INORGANIC) CLUSTER × 2 FOR FORMYL GROUP × 10 GOL GLYCEROL × 4 CL CHLORIDE ION × 7 MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Mes-NaOH (pH 6), 0.4M MgCl2, 20% PEG4000, 20% glyerol
Resolution 1.53 Å R-free 0.194
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 515–518（4 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
9RJ9 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.45 Å R-free 0.191
9RJ9 [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.45 Å R-free 0.191
9RJO [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.67 Å R-free 0.206
9RJO [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；20% PEG 4000, 0.4 M MgCl2,0.1 M MES, 20 % glycerol
Resolution 1.67 Å R-free 0.206
9RJQ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.75 Å R-free 0.220
9RJQ [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L Deposited 2025-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–574（574 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 4 FES FE2/S2 (INORGANIC) CLUSTER × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；21% PEG 4000, 0.4 M MgCl2,0.1 M MES (pH6), 19 % glycerol
Resolution 1.75 Å R-free 0.220

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

View Construct and Data Evidence
UniProt name PHF1_CLOPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–574； UniProt 1–574

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

SAXS scattering curve SAXS Profile

SAXS profile for 3c8y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3c8y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3c8y
Deposition date deposition_date2008-02-14
Structure title title1.39 Angstrom crystal structure of Fe-only hydrogenase
Keywords keywordsdithiomethylether, H-cluster, hydrogenase, Iron, Iron-sulfur, Metal-binding, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.46 Å
Radius of gyration Rg (electron density) rg_electron24.95 Å
Forward intensity I(0) i078365500.00
Molecular weight molecular_weight66060.0 kDa
Excluded volume excluded_volume81122 ų
Envelope volume envelope_volume94530 ų
Hydration-shell volume shell_volume31194 ų
Envelope diameter envelope_diameter84.7 Å
Shell Rg shell_rg32.73 Å
Envelope Rg envelope_rg25.45 Å
Shape Rg shape_rg25.09 Å
Total Rg total_rg25.29 Å
Total atoms total_atoms4533
Residues n_residues574
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.3 Å
Rg (real space) rg_real25.46 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real7.8370e+07
I(0) uncertainty (real space) i0_real_error1.2250e+06
Rg (reciprocal space) rg_reciprocal25.46 Å
I(0) (reciprocal space) i0_reciprocal78370000.0000
Solution quality estimate total_estimate0.6922
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.397
Kurtosis Kurtosis kurtosis-0.268
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25480000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 0.164; Positv: 1.000; Valcen: 0.996; Smooth: 0.932
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3c8ya1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.96 — Fe-only hydrogenase
Superfamily Superfamily superfamilyc.96.1 — Fe-only hydrogenase
Family Family familyc.96.1.1 — Fe-only hydrogenase
Domain ID domain_idd3c8ya2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
Family Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
Domain ID domain_idd3c8ya3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins

CATH v4.4 (2 domains)

Domain ID domain_id3c8yA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily740 —
Domain ID domain_id3c8yA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)