4ko3

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） IRON/SULFUR CLUSTER × 3 CALCIUM ION × 3 CHLORIDE ION × 1 GLYCEROL × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 HYDROSULFURIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） IRON/SULFUR CLUSTER × 3 CALCIUM ION × 5 GLYCEROL × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 HYDROSULFURIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） IRON/SULFUR CLUSTER × 3 CALCIUM ION × 3 CHLORIDE ION × 1 GLYCEROL × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 HYDROSULFURIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） IRON/SULFUR CLUSTER × 3 CALCIUM ION × 5 GLYCEROL × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 HYDROSULFURIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ko3
Deposition date deposition_date	2013-05-11
Structure title title	Low 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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4ko3__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ko3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ko3__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.54 Å
Rg (electron density)	24.51 Å
Total Rg	25.33 Å
Atom count	5993
Residues	767
Excluded volume	107090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ko3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ko3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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	14236

MTEGAKKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKGHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE

Entity 2 Entity 2 polymer

Description description	Nickel-dependent hydrogenase large subunit
Molecular weight formula_weight	55323.8 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	1843

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ko3l_
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	d4ko3m_
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	d4ko3s_
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	d4ko3t_
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	4ko3L00
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	4ko3M00
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	4ko3S01
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	4ko3S02
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	4ko3T01
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	4ko3T02
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

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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	1.700 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1657
R_work r_work	0.1638
R_free r_free	0.2007

Low 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ko3__assembly_2__model_1

4ko3__assembly_2__model_1 | I(q)

4ko3__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Low 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nickel-dependent hydrogenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ko3__assembly_2__model_1

4ko3__assembly_2__model_1 | I(q)

4ko3__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (2)