SAXSdb — 2wbp

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

L-ARGININE BETA-HYDROXYLASE

STREPTOMYCES VINACEUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ARGININE × 1 FE (II) ION × 1 (2S,3S)-3-HYDROXYARGININE × 1 SUCCINIC ACID × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6WZB0_STRVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–358； UniProt 1–358

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	2wbp
Deposition date deposition_date	2009-03-02
Structure title title	Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate
Keywords keywords	OXIDOREDUCTASE, NON-HEME FE(II) HYDROXYLASE, CBETA-HYDROXYLATION, NRPS, VIOMYCIN, ALPHA-KETOGLUTARATE; 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.

2wbp__assembly_1__model_1

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

Download this curve (.dat)

2wbp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wbp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.52 Å
Rg (electron density)	19.44 Å
Total Rg	20.36 Å
Atom count	2635
Residues	333
Excluded volume	46202 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wbp__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 (7)

Entity 1 Entity 1 polymer

Description description	L-ARGININE BETA-HYDROXYLASE
Molecular weight formula_weight	39481.2 kDa
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	3171

MTESPTTHHGAAPPDSVATPVRPWSEFRLTPAEAAAAAALAARCAQRYDETDGPEFLLDAPVIAHELPRRLRTFMARARLDAWPHALVVRGNPVDDAALGSTPVHWRTARTPGSRPLSFLLMLYAGLLGDVFGWATQQDGRVVTDVLPIKGGEHTLVSSSSRQELGWHTEDAFSPYRADYVGLLSLRNPDGVATTLAGVPLDDLDERTLDVLFQERFLIRPDDSHLQVNNSTAQQGRVEFEGIAQAADRPEPVAILTGHRAAPHLRVDGDFSAPAEGDEEAAAALGTLRKLIDASLYELVLDQGDVAFIDNRRAVHGRRAFQPRYDGRDRWLKRINITRDLHRSRKAWAGDSRVLGQR

Source Source

Source organism organism	STREPTOMYCES VINACEUS
NCBI taxonomy ID ncbi_taxonomy_id	1960
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	(2S,3S)-3-HYDROXYARGININE
Molecular weight formula_weight	190.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 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	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	387

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2wbpA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

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Unit-cell length a length_a	80.770 Å
Unit-cell length b length_b	66.930 Å
Unit-cell length c length_c	62.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.16 °
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	1.160 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.1329
R_work r_work	0.1322
R_free r_free	0.1710

Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate

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

L-ARGININE BETA-HYDROXYLASE

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

2wbp__assembly_1__model_1

2wbp__assembly_1__model_1 | I(q)

2wbp__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

Source Source

Entity 2 Entity 2 non-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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate

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

L-ARGININE BETA-HYDROXYLASE

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

2wbp__assembly_1__model_1

2wbp__assembly_1__model_1 | I(q)

2wbp__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

Source Source

Entity 2 Entity 2 non-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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)