4ko4

High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Method: X-RAY DIFFRACTION D_max: 120.5 Å Quality: GOOD

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

Periplasmic [NiFeSe] hydrogenase small subunit

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain S； UniProt 33–315	Not recorded	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.172
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain T； UniProt 33–315	Not recorded	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.172

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 4KO4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CC1 CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM Deposited 1999-03-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 NI NICKEL (II) ION × 1 FE2 FE (II) ION × 1 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；pH 6.2	Resolution 2.15 Å R-free 0.248
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.52 Å R-free 0.171
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-07	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.52 Å R-free 0.171
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-09	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.168
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-09	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.168
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.55 Å R-free 0.184
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.55 Å R-free 0.184
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.194
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.194
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.201
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 33–315（283 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.201

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHSS_DESBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain S； PDBConstruct 1–283； UniProt 33–315 Author chain T； PDBConstruct 1–283； UniProt 33–315

Nickel-dependent hydrogenase large subunit

OrganismNot specified

UniProt C7LN88

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 1–499	Not recorded	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.172
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 1–499	Not recorded	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.172

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4KO4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–499（499 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.52 Å R-free 0.171
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–499（499 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.52 Å R-free 0.171
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-09	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.168
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-09	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.168
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.55 Å R-free 0.184
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.55 Å R-free 0.184
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.194
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–499（499 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.194
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–499（499 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.201
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air Deposited 2013-05-11	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–499（499 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.201

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C7LN88_DESBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–499； UniProt 1–499 Author chain M； PDBConstruct 1–499； UniProt 1–499

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	4ko4
Deposition date deposition_date	2013-05-11
Structure title title	High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Keywords keywords	NIFESE-SITE, H2 CLEAVAGE/PRODUCTION, SELENINATE, 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	37.09 Å
Radius of gyration Rg (electron density) rg_electron	36.59 Å
Forward intensity I(0) i0	450765000.00
Molecular weight molecular_weight	171890.0 kDa
Excluded volume excluded_volume	214110 Å³
Envelope volume envelope_volume	252750 Å³
Hydration-shell volume shell_volume	56360 Å³
Envelope diameter envelope_diameter	126.2 Å
Shell Rg shell_rg	43.71 Å
Envelope Rg envelope_rg	36.47 Å
Shape Rg shape_rg	36.58 Å
Total Rg total_rg	37.02 Å
Total atoms total_atoms	11985
Residues n_residues	1534
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	120.5 Å
Rg (real space) rg_real	37.13 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	4.5080e+08
I(0) uncertainty (real space) i0_real_error	7.0780e+06
Rg (reciprocal space) rg_reciprocal	37.11 Å
I(0) (reciprocal space) i0_reciprocal	450800000.0000
Solution quality estimate total_estimate	0.8826
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.4 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	149900000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.862

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Periplasmic [NiFeSe] hydrogenase small subunit
Molecular weight formula_weight	30874.1 kDa
EC 编号 ec_number	1.12.99.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T
Atom count atom_count	14237

MTEGAKKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKGHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE

Entity 2 Entity 2 polymer

Description description	Nickel-dependent hydrogenase large subunit
Molecular weight formula_weight	55291.8 kDa
EC 编号 ec_number	1.18.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSQAATPAADGKVKISIDPLTRVEGHLKIEVEVKDGKVVDAKCSGGMFRGFEQILRGRDPRDSSQIVQRICGVCPTAHCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVPRYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSFFDHSAPGGLHYSVGETNPNPDKPGAYSFVKAPRYKDKPCEVGPLARMWVQNPELSPVGQKLLKELYGIEAKNFRDLGDKAFSIMGRHVARAEETWLTAVAVEKWLKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPVNVGRLVRSYDPULGCAVH

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	6

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	CARBONMONOXIDE-(DICYANO) IRON
Molecular weight formula_weight	135.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1844

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ko4l_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

Domain ID domain_id	d4ko4m_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

Domain ID domain_id	d4ko4s_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

Domain ID domain_id	d4ko4t_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

CATH v4.4 (6 domains)

Domain ID domain_id	4ko4L00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	4ko4M00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	4ko4S01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	4ko4S02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

Domain ID domain_id	4ko4T01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	4ko4T02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	106.200 Å
Unit-cell length b length_b	108.720 Å
Unit-cell length c length_c	136.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1495
R_work r_work	0.1484
R_free r_free	0.1719

fit	/app/data/saxs_computation/ko/4ko4/4ko4.fit
pddf	/app/data/pr_computation/ko/4ko4/4ko4.pr.out
profile	/app/data/saxs_computation/ko/4ko4/4ko4.dat

High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

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

Periplasmic [NiFeSe] hydrogenase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Nickel-dependent hydrogenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)