SAXSdb — 1w9m

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

HYDROXYLAMINE REDUCTASE

DESULFOVIBRIO VULGARIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 FE-S-O HYBRID CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIS_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–553； UniProt 1–553

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	1w9m
Deposition date deposition_date	2004-10-14
Structure title title	AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal
Keywords keywords	HYBRID CLUSTER PROTEIN, ANAEROBIC, OXIDISED, AS-ISOLATED, DESULFOVIBRIO VULGARIS, 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.

1w9m__assembly_1__model_1

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

Download this curve (.dat)

1w9m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w9m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.94 Å
Rg (electron density)	23.13 Å
Total Rg	23.78 Å
Atom count	4235
Residues	552
Excluded volume	76104 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w9m__assembly_1__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	HYDROXYLAMINE REDUCTASE
Molecular weight formula_weight	60074.7 kDa
EC 编号 ec_number	1.7.-.-
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	5065

MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGCDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK

Source Source

Source organism organism	DESULFOVIBRIO VULGARIS
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	DESULFOVIBRIO VULGARIS

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FE-S-O HYBRID CLUSTER
Molecular weight formula_weight	335.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	789

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1w9ma_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.1 — Hybrid cluster protein (prismane protein)

CATH v4.4 (4 domains)

Domain ID domain_id	1w9mA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1w9mA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1w9mA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1w9mA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

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Unit-cell length a length_a	64.270 Å
Unit-cell length b length_b	66.843 Å
Unit-cell length c length_c	134.764 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	1.350 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.1282
R_work r_work	—
R_free r_free	0.1774

AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal

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

HYDROXYLAMINE REDUCTASE

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

1w9m__assembly_1__model_1

1w9m__assembly_1__model_1 | I(q)

1w9m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)

AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal

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

HYDROXYLAMINE REDUCTASE

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

1w9m__assembly_1__model_1

1w9m__assembly_1__model_1 | I(q)

1w9m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)