SAXSdb — 2vvq

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

RIBOSE-5-PHOSPHATE ISOMERASE B

MYCOBACTERIUM TUBERCULOSIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5-O-phosphono-D-ribonic acid × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	5-O-phosphono-D-ribonic acid × 2 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	5-O-phosphono-D-ribonic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPIB_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain B； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162 Author chain D； PDBConstruct 1–162； UniProt 1–162 Author chain E； PDBConstruct 1–162； UniProt 1–162

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	2vvq
Deposition date deposition_date	2008-06-10
Structure title title	Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate
Keywords keywords	PENTOSE PHOSPHATE PATHWAY, RPIB, RV2465C, ISOMERASE, CARBOHYDRATE METABOLISM; ISOMERASE
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.

2vvq__assembly_1__model_1

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

Download this curve (.dat)

2vvq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vvq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.14 Å
Rg (electron density)	18.15 Å
Total Rg	19.02 Å
Atom count	2395
Residues	314
Excluded volume	41915 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vvq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vvq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vvq__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	RIBOSE-5-PHOSPHATE ISOMERASE B
Molecular weight formula_weight	17299.5 kDa
EC 编号 ec_number	5.3.1.6
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	6547

MSGMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPGAPA

Source Source

Source organism organism	MYCOBACTERIUM TUBERCULOSIS
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	5-O-phosphono-D-ribonic acid
Molecular weight formula_weight	246.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	547

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2vvqa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
Superfamily Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
Family Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

Domain ID domain_id	d2vvqb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
Superfamily Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
Family Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

Domain ID domain_id	d2vvqc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
Superfamily Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
Family Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

Domain ID domain_id	d2vvqd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
Superfamily Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
Family Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

Domain ID domain_id	d2vvqe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.121 — Ribose/Galactose isomerase RpiB/AlsB
Superfamily Superfamily superfamily	c.121.1 — Ribose/Galactose isomerase RpiB/AlsB
Family Family family	c.121.1.1 — Ribose/Galactose isomerase RpiB/AlsB

CATH v4.4 (5 domains)

Domain ID domain_id	2vvqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	2vvqB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	2vvqC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	2vvqD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	2vvqE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

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Unit-cell length a length_a	136.369 Å
Unit-cell length b length_b	102.119 Å
Unit-cell length c length_c	69.604 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1610
R_work r_work	0.1590
R_free r_free	0.1930

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate

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

RIBOSE-5-PHOSPHATE ISOMERASE B

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

2vvq__assembly_1__model_1

2vvq__assembly_1__model_1 | I(q)

2vvq__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate

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

RIBOSE-5-PHOSPHATE ISOMERASE B

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

2vvq__assembly_1__model_1

2vvq__assembly_1__model_1 | I(q)

2vvq__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)