4xdc

Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor

Method: X-RAY DIFFRACTION D_max: 104.0 Å Quality: GOOD

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

Iron hydrogenase 1

Clostridium pasteurianum

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

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 4XDC	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
3C8Y 1.39 Angstrom crystal structure of Fe-only hydrogenase Deposited 2008-02-14	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
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 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 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 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 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 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 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 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 60 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 Author chain B； 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

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4xdc
Deposition date deposition_date	2014-12-19
Structure title title	Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor
Keywords keywords	Hydrogenase, H-cluster, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.25 Å
Radius of gyration Rg (electron density) rg_electron	31.94 Å
Forward intensity I(0) i0	302904000.00
Molecular weight molecular_weight	132840.0 kDa
Excluded volume excluded_volume	163020 Å³
Envelope volume envelope_volume	199760 Å³
Hydration-shell volume shell_volume	50588 Å³
Envelope diameter envelope_diameter	108.4 Å
Shell Rg shell_rg	40.12 Å
Envelope Rg envelope_rg	31.79 Å
Shape Rg shape_rg	32.11 Å
Total Rg total_rg	31.99 Å
Total atoms total_atoms	18048
Residues n_residues	1159
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	104.0 Å
Rg (real space) rg_real	32.15 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	3.0290e+08
I(0) uncertainty (real space) i0_real_error	4.3230e+06
Rg (reciprocal space) rg_reciprocal	32.20 Å
I(0) (reciprocal space) i0_reciprocal	302900000.0000
Solution quality estimate total_estimate	0.8879
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.3 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.338
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	82790000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.868

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Iron hydrogenase 1
Molecular weight formula_weight	65111.4 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	19338

MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQFEK

来源 Source

来源生物 organism	Clostridium pasteurianum
NCBI Class编号 ncbi_taxonomy_id	1501
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
Molecular weight formula_weight	355.0 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	2

来源 Source

来源生物 organism	Clostridium pasteurianum
NCBI Class编号 ncbi_taxonomy_id	1501
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1227

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4xdca1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.0 — automated matches

Domain ID domain_id	d4xdca2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d4xdca3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d4xdca4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4xdcb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.0 — automated matches

Domain ID domain_id	d4xdcb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d4xdcb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d4xdcb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4xdcA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	4xdcA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4xdcB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	4xdcB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	91.340 Å
Unit-cell length b length_b	73.650 Å
Unit-cell length c length_c	103.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.630 Å
Low-resolution limit resolution_low	47.445 Å
R factor r_factor	0.1515
R_work r_work	0.1502
R_free r_free	0.1756

fit	/app/data/saxs_computation/xd/4xdc/4xdc.fit
pddf	/app/data/pr_computation/xd/4xdc/4xdc.pr.out
profile	/app/data/saxs_computation/xd/4xdc/4xdc.dat

Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor

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

Iron hydrogenase 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)