3oqt

Crystal structure of Rv1498A protein from mycobacterium tuberculosis

Method: X-RAY DIFFRACTION

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

Rv1498A PROTEIN

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	CHLORIDE ION × 6 SODIUM ION × 3 water × 12	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	CHLORIDE ION × 6 SODIUM ION × 3 water × 12	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 12	CHLORIDE ION × 6 SODIUM ION × 6 water × 12	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 12	CHLORIDE ION × 6 SODIUM ION × 3 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VK10_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 1–70 Author chain B； PDBConstruct 1–70； UniProt 1–70 Author chain C； PDBConstruct 1–70； UniProt 1–70 Author chain D； PDBConstruct 1–70； UniProt 1–70 Author chain E； PDBConstruct 1–70； UniProt 1–70 Author chain F； PDBConstruct 1–70； UniProt 1–70 Author chain G； PDBConstruct 1–70； UniProt 1–70 Author chain H； PDBConstruct 1–70； UniProt 1–70 Author chain I； PDBConstruct 1–70； UniProt 1–70 Author chain J； PDBConstruct 1–70； UniProt 1–70 Author chain K； PDBConstruct 1–70； UniProt 1–70 Author chain L； PDBConstruct 1–70； UniProt 1–70 Author chain M； PDBConstruct 1–70； UniProt 1–70 Author chain N； PDBConstruct 1–70； UniProt 1–70 Author chain O； PDBConstruct 1–70； UniProt 1–70 Author chain P； PDBConstruct 1–70； UniProt 1–70

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	3oqt
Deposition date deposition_date	2010-09-04
Structure title title	Crystal structure of Rv1498A protein from mycobacterium tuberculosis
Keywords keywords	DODECIN, FLAVIN BINDING, FLAVOPROTEIN; FLAVOPROTEIN
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.

3oqt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3oqt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oqt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.90 Å
Rg (electron density)	26.20 Å
Total Rg	27.03 Å
Atom count	6441
Residues	840
Excluded volume	113520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oqt__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oqt__assembly_2__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3oqt__assembly_3__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3oqt__assembly_4__model_1`	dodecameric （12）	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	Rv1498A PROTEIN
Molecular weight formula_weight	7637.6 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	8856

MSNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLEDS

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3oqta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqte_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqth_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqti_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqto_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d3oqtp_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	3oqtA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtN00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	3oqtP00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

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Unit-cell length a length_a	143.946 Å
Unit-cell length b length_b	143.946 Å
Unit-cell length c length_c	143.946 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	192

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2538
R_work r_work	0.2522
R_free r_free	0.2828

Crystal structure of Rv1498A protein from mycobacterium tuberculosis

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

Rv1498A PROTEIN

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

3oqt__assembly_2__model_1

3oqt__assembly_2__model_1 | I(q)

3oqt__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of Rv1498A protein from mycobacterium tuberculosis

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

Rv1498A PROTEIN

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

3oqt__assembly_2__model_1

3oqt__assembly_2__model_1 | I(q)

3oqt__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)