SAXSdb — 1h2r

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

PROTEIN (PERIPLASMIC [NIFE] 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	PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT) × 1 （P21852） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 MAGNESIUM ION × 1 NI-FE ACTIVE CENTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNS_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain S； PDBConstruct 1–267； UniProt 51–317

PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)

OrganismNot specified

UniProt P21852

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) × 1 （P21853） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 MAGNESIUM ION × 1 NI-FE ACTIVE CENTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNL_DESVM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–534； UniProt 19–552

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	1h2r
Deposition date deposition_date	1999-06-14
Structure title title	THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION
Keywords keywords	;HIGH RESOLUTION CRYSTAL STRUCTURE, SULFUR-BRIDGING LIGAND, NI-FE HYDROGENASE, REDUCED ENZYME, ATOMIC CAP AT ACTIVE SITE, 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.

1h2r__assembly_1__model_1

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

Download this curve (.dat)

1h2r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h2r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.90 Å
Rg (electron density)	24.90 Å
Total Rg	25.70 Å
Atom count	6226
Residues	801
Excluded volume	110950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h2r__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 (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)
Molecular weight formula_weight	28789.7 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S
Atom count atom_count	6803

LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN

Entity 2 Entity 2 polymer

Description description	PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)
Molecular weight formula_weight	59179.3 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

SSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNNVSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVH

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	2

Entity 4 Entity 4 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 6 Entity 6 non-polymer

Description description	NI-FE ACTIVE CENTER
Molecular weight formula_weight	251.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	577

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1h2rl_
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	d1h2rs_
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	1h2rL00
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	1h2rS01
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	1h2rS02
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	100.440 Å
Unit-cell length b length_b	126.860 Å
Unit-cell length c length_c	66.680 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	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2540

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION

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

PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (PERIPLASMIC [NIFE] 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

1h2r__assembly_1__model_1

1h2r__assembly_1__model_1 | I(q)

1h2r__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (3)

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION

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

PROTEIN (PERIPLASMIC [NIFE] 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

PROTEIN (PERIPLASMIC [NIFE] 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

1h2r__assembly_1__model_1

1h2r__assembly_1__model_1 | I(q)

1h2r__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (3)