5jsy

The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution

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 str. Hildenborough

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 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 1–317； UniProt 1–317

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

Desulfovibrio vulgaris str. Hildenborough

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 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 9–507； UniProt 12–510

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	5jsy
Deposition date deposition_date	2016-05-09
Structure title title	The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution
Keywords keywords	NIFESE-SITE H2 CLEAVAGE/PRODUCTION, 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.

5jsy__assembly_1__model_1

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

Download this curve (.dat)

5jsy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jsy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.20 Å
Rg (electron density)	24.30 Å
Total Rg	25.12 Å
Atom count	11693
Residues	764
Excluded volume	105530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jsy__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Description description	Periplasmic [NiFeSe] hydrogenase, small subunit
Molecular weight formula_weight	33940.9 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13393

MSLTRRDFVKLCTGTVAGFGISQMFHPAVHEALAGTLTGERPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA

Source Source

Source organism organism	Desulfovibrio vulgaris str. Hildenborough
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	55958.1 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WSHPQFEKGATGRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPCLGCAVHVLHAESGKVAVIEVK

Source Source

Source organism organism	Desulfovibrio vulgaris str. Hildenborough
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	3

Entity 4 Entity 4 non-polymer

Description description	CARBONMONOXIDE-(DICYANO) IRON
Molecular weight formula_weight	135.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	988

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5jsya_
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 (3 domains)

Domain ID domain_id	5jsyA01
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	5jsyA02
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	5jsyB00
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	106.324 Å
Unit-cell length b length_b	62.857 Å
Unit-cell length c length_c	110.823 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.040 Å
Low-resolution limit resolution_low	29.200 Å
R factor r_factor	0.1123
R_work r_work	0.1115
R_free r_free	0.1275

The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution

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

5jsy__assembly_1__model_1

5jsy__assembly_1__model_1 | I(q)

5jsy__assembly_1__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution

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

5jsy__assembly_1__model_1

5jsy__assembly_1__model_1 | I(q)

5jsy__assembly_1__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)