SAXSdb — 6dax

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

Alpha-ketoglutarate-dependent L-arginine hydroxylase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-OXOGLUTARIC ACID × 1 L-HOMOARGININE × 1 FE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARGHX_STRVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 21–358

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	6dax
Deposition date deposition_date	2018-05-02
Structure title title	X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate
Keywords keywords	desaturase, hydroxylase, oxygenase, metalloenzyme, desaturation, hydroxylation, viomycin, 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.

6dax__assembly_1__model_1

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

Download this curve (.dat)

6dax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dax__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.61 Å
Rg (electron density)	19.50 Å
Total Rg	20.42 Å
Atom count	2671
Residues	338
Excluded volume	46790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dax__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 (5)

Entity 1 Entity 1 polymer

Description description	Alpha-ketoglutarate-dependent L-arginine hydroxylase
Molecular weight formula_weight	37493.1 kDa
EC 编号 ec_number	1.14.11.41
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2766

VRPWSEFRLTPAEAAAAAALAARCAQRYDETDGPEFLLDAPVIAHELPRRLRTFMARARLDAWPHALVVRGNPVDDAALGSTPVHWRTARTPGSRPLSFLLMLYAGLLGDVFGWATQQDGRVVTDVLPIKGGEHTLVSSSSRQELGWHTEDAFSPYRADYVGLLSLRNPDGVATTLAGVPLDDLDERTLDVLFQERFLIRPDDSHLQVNNSTAQQGRVEFEGIAQAADRPEPVAILTGHRAAPHLRVDGDFSAPAEGDEEAAAALGTLRKLIDASLYELVLDQGDVAFIDNRRAVHGRRAFQPRYDGRDRWLKRINITRDLHRSRKAWAGDSRVLGQR

Entity 2 Entity 2 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	L-HOMOARGININE
Molecular weight formula_weight	188.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6daxA00
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	80.376 Å
Unit-cell length b length_b	67.076 Å
Unit-cell length c length_c	62.646 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.72 °
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	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2161
R_work r_work	0.2157
R_free r_free	0.2238

X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate

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

Alpha-ketoglutarate-dependent L-arginine 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

6dax__assembly_1__model_1

6dax__assembly_1__model_1 | I(q)

6dax__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate

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

Alpha-ketoglutarate-dependent L-arginine 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

6dax__assembly_1__model_1

6dax__assembly_1__model_1 | I(q)

6dax__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)