6z9g

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2

Method: X-RAY DIFFRACTION

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

Periplasmic [NiFeSe] hydrogenase, small subunit

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)

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, large subunit, selenocysteine-containing × 1 （Q72AS3） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing × 1 （Q72AS3） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing × 1 （Q72AS3） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing × 1 （Q72AS3） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72AS4_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 35–317 Author chain C； PDBConstruct 1–283； UniProt 35–317 Author chain E； PDBConstruct 1–283； UniProt 35–317 Author chain G； PDBConstruct 1–283； UniProt 35–317

Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)

UniProt Q72AS3

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 （Q72AS4） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, small subunit × 1 （Q72AS4） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, small subunit × 1 （Q72AS4） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFeSe] hydrogenase, small subunit × 1 （Q72AS4） IRON/SULFUR CLUSTER × 3 oxygen-damaged SF4 × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 FE (II) ION × 1 HYDROSULFURIC ACID × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72AS3_DESVH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–484； UniProt 12–495 Author chain D； PDBConstruct 1–484； UniProt 12–495 Author chain F； PDBConstruct 1–484； UniProt 12–495 Author chain H； PDBConstruct 1–484； UniProt 12–495

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	6z9g
Deposition date deposition_date	2020-06-03
Structure title title	Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2
Keywords keywords	Hydrogenase, Selenium, gas channels, high-pressure derivatization, 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.

6z9g__assembly_2__model_1

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

Download this curve (.dat)

6z9g__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z9g__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.10 Å
Rg (electron density)	24.23 Å
Total Rg	25.02 Å
Atom count	11618
Residues	758
Excluded volume	104790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z9g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6z9g__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6z9g__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6z9g__assembly_4__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	30261.6 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	47993

GTLTGERPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA

Source Source

Source organism organism	Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	Desulfovibrio vulgaris str. Hildenborough

Entity 2 Entity 2 polymer

Description description	Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
Molecular weight formula_weight	53365.1 kDa
EC 编号 ec_number	1.12.7.2
Mutation mutation	G491A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GATGRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPULACAVH

Source Source

Source organism organism	Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	Desulfovibrio vulgaris str. Hildenborough

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	12

Entity 4 Entity 4 non-polymer

Description description	oxygen-damaged SF4
Molecular weight formula_weight	383.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CARBONMONOXIDE-(DICYANO) IRON
Molecular weight formula_weight	135.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	946

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6z9ga_
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	d6z9gb_
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	d6z9gc_
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	d6z9gd_
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	d6z9ge_
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	d6z9gf_
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	d6z9gg_
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	d6z9gh_
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

CATH v4.4 (3 domains)

Domain ID domain_id	6z9gD01
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	6z9gF01
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	6z9gH01
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

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Unit-cell length a length_a	120.306 Å
Unit-cell length b length_b	93.815 Å
Unit-cell length c length_c	126.951 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	61.200 Å
R factor r_factor	0.1944
R_work r_work	0.1920
R_free r_free	0.2397

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2

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

Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing

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

6z9g__assembly_2__model_1

6z9g__assembly_2__model_1 | I(q)

6z9g__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2

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

Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing

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

6z9g__assembly_2__model_1

6z9g__assembly_2__model_1 | I(q)

6z9g__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)