SAXSdb — 2vvo

▼

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	6-O-phosphono-alpha-D-allopyranose × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	6-O-phosphono-alpha-D-allopyranose × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	6-O-phosphono-alpha-D-allopyranose × 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vvo
Deposition date deposition_date	2008-06-10
Structure title title	Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha d-allose 6-phosphate
Keywords keywords	RPIB, RV2465C, ISOMERASE, RARE SUGAR, CARBOHYDRATE METABOLISM, PENTOSE PHOSPHATE PATHWAY; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2vvo__assembly_2__model_1

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

Download this curve (.dat)

2vvo__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vvo__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.26 Å
Rg (electron density)	18.27 Å
Total Rg	19.13 Å
Atom count	2392
Residues	314
Excluded volume	41912 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vvo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vvo__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vvo__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

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	6397

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	6-O-phosphono-alpha-D-allopyranose
Molecular weight formula_weight	260.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2vvoa_
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	d2vvob_
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	d2vvoc_
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	d2vvod_
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	d2vvoe_
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	2vvoA00
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	2vvoB00
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	2vvoC00
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	2vvoD00
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	2vvoE00
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

▶

Unit-cell length a length_a	152.744 Å
Unit-cell length b length_b	92.501 Å
Unit-cell length c length_c	60.967 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.92 °
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	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1620
R_work r_work	0.1600
R_free r_free	0.1960

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha d-allose 6-phosphate

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

2vvo__assembly_2__model_1

2vvo__assembly_2__model_1 | I(q)

2vvo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 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 alpha d-allose 6-phosphate

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

2vvo__assembly_2__model_1

2vvo__assembly_2__model_1 | I(q)

2vvo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)