3vb9

Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109

Method: X-RAY DIFFRACTION

▼

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

Uncharacterized protein VPA0735

Vibrio parahaemolyticus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87I71_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–483； UniProt 1–483 Author chain B； PDBConstruct 1–483； UniProt 1–483 Author chain C； PDBConstruct 1–483； UniProt 1–483 Author chain D； PDBConstruct 1–483； UniProt 1–483

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	3vb9
Deposition date deposition_date	2011-12-31
Structure title title	Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109
Keywords keywords	Structural Genomics, PSI-Biology, Northeast Structural Genomics Consortium, NESG, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3vb9__assembly_1__model_1

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

Download this curve (.dat)

3vb9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vb9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.32 Å
Rg (electron density)	32.16 Å
Total Rg	32.53 Å
Atom count	7457
Residues	894
Excluded volume	133160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vb9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vb9__assembly_2__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	Uncharacterized protein VPA0735
Molecular weight formula_weight	55936.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15733

MKKRILAVAVTSMLLSASVFAQETVVPSRVGDLKFESDFPTQETMKNMLNEMDFQRATQAYLWGIPASSIMEWLNVSRNDFKFEEGQMGFFNTLKQKQGIITANFTTPYVIGTWNLEKTGPLIINLPEAKMAGMMLDVHQRVLSDLSLLGPDKGKGGKYLIVPPGEKYKDLNPKGYYVIRPKTNVVYGGIRILEPDVDRVVKQVVPNITTQPYADGKLGRKIPVAQVPEIDWTHIPKDGLEYWKTIHQIIQENPVEERDRFVMAQLKFLGIEKGKPFNPTEEQKKILLEASKVGRAMAQSNDYTKRFTQPYWKGTNWKDAISVSLDQRSENYDELDERAAWFYEAITVSRGMKSTIPGFGQRYLVTYQDSDGNWLSGEHTYKLHVPANVPASNFWSTTVYDENNRLMIINDAGSPDISSRKNLKVNSDGSIDVYYGPKPVKGYENNWVQTNPGEGWFTYFRFYGPTEKMFDKSWTMGDIELVK

Source Source

Source organism organism	Vibrio parahaemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	670
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	839

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3vb9a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.65 — VPA0735-like
Superfamily Superfamily superfamily	e.65.1 — VPA0735-like
Family Family family	e.65.1.1 — VPA0735-like

Domain ID domain_id	d3vb9b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.65 — VPA0735-like
Superfamily Superfamily superfamily	e.65.1 — VPA0735-like
Family Family family	e.65.1.1 — VPA0735-like

Domain ID domain_id	d3vb9c_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.65 — VPA0735-like
Superfamily Superfamily superfamily	e.65.1 — VPA0735-like
Family Family family	e.65.1.1 — VPA0735-like

Domain ID domain_id	d3vb9d_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.65 — VPA0735-like
Superfamily Superfamily superfamily	e.65.1 — VPA0735-like
Family Family family	e.65.1.1 — VPA0735-like

CATH v4.4 (16 domains)

Domain ID domain_id	3vb9A01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3vb9A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3360 — VPA0735-like fold
Homologous superfamily homologous superfamily	10 — VPA0735-like domain

Domain ID domain_id	3vb9A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1610 — Domain of unknown function DUF1254

Domain ID domain_id	3vb9A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	600 — Domain of unknown function DUF1214, C-terminal domain

Domain ID domain_id	3vb9B01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3vb9B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3360 — VPA0735-like fold
Homologous superfamily homologous superfamily	10 — VPA0735-like domain

Domain ID domain_id	3vb9B03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1610 — Domain of unknown function DUF1254

Domain ID domain_id	3vb9B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	600 — Domain of unknown function DUF1214, C-terminal domain

Domain ID domain_id	3vb9C01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3vb9C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3360 — VPA0735-like fold
Homologous superfamily homologous superfamily	10 — VPA0735-like domain

Domain ID domain_id	3vb9C03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1610 — Domain of unknown function DUF1254

Domain ID domain_id	3vb9C04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	600 — Domain of unknown function DUF1214, C-terminal domain

Domain ID domain_id	3vb9D01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3vb9D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3360 — VPA0735-like fold
Homologous superfamily homologous superfamily	10 — VPA0735-like domain

Domain ID domain_id	3vb9D03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1610 — Domain of unknown function DUF1254

Domain ID domain_id	3vb9D04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	600 — Domain of unknown function DUF1214, C-terminal domain

▶

Unit-cell length a length_a	63.267 Å
Unit-cell length b length_b	106.929 Å
Unit-cell length c length_c	157.178 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	39.990 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2740

Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109

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

Uncharacterized protein VPA0735

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

3vb9__assembly_1__model_1

3vb9__assembly_1__model_1 | I(q)

3vb9__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 (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) 20 domains

SCOP 2.08 (4 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109

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

Uncharacterized protein VPA0735

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

3vb9__assembly_1__model_1

3vb9__assembly_1__model_1 | I(q)

3vb9__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 (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) 20 domains

SCOP 2.08 (4 domains)

CATH v4.4 (16 domains)

7. Citations (1)