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5la3

[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A

Method: X-RAY DIFFRACTION Dmax: 103.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Iron hydrogenase 1

Clostridium pasteurianum

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 2–574 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–574 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

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

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View Construct and Data Evidence
UniProt name PHF1_CLOPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–573； UniProt 2–574 Author chain B； PDBConstruct 1–573； UniProt 2–574

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 5la3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5la3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5la3
Deposition date deposition_date2016-06-13
Structure title title[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E279A
Keywords keywordsHydrogenase, H-cluster, OXIDOREDUCTASE, semisynthetic enzyme; 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_guinier32.42 Å
Radius of gyration Rg (electron density) rg_electron32.13 Å
Forward intensity I(0) i0296439000.00
Molecular weight molecular_weight131460.0 kDa
Excluded volume excluded_volume161400 ų
Envelope volume envelope_volume199270 ų
Hydration-shell volume shell_volume50260 ų
Envelope diameter envelope_diameter108.5 Å
Shell Rg shell_rg40.12 Å
Envelope Rg envelope_rg32.02 Å
Shape Rg shape_rg32.30 Å
Total Rg total_rg32.17 Å
Total atoms total_atoms9026
Residues n_residues1149
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 dmax103.6 Å
Rg (real space) rg_real32.34 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real2.9640e+08
I(0) uncertainty (real space) i0_real_error5.1820e+06
Rg (reciprocal space) rg_reciprocal32.38 Å
I(0) (reciprocal space) i0_reciprocal296400000.0000
Solution quality estimate total_estimate0.6759
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.2 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90740000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.999; Smooth: 0.781
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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) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5la3a1
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.15.4.0 — automated matches
Domain ID domain_idd5la3a2
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.58.1.0 — automated matches
Domain ID domain_idd5la3a3
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_idd5la3a4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5la3b1
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.15.4.0 — automated matches
Domain ID domain_idd5la3b2
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.58.1.0 — automated matches
Domain ID domain_idd5la3b3
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_idd5la3b4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5la3A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily740 —
Domain ID domain_id5la3A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id5la3B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily740 —
Domain ID domain_id5la3B02
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)