SAXSdb — 2od0

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

Hypothetical protein VP1028

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 × 2 SULFATE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87QX1_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 1–105 Author chain B； PDBConstruct 1–105； UniProt 1–105

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	2od0
Deposition date deposition_date	2006-12-21
Structure title title	The crystal structure of gene product VP1028 from Vibrio parahaemolyticus
Keywords keywords	;Structural genomics, Vibrio parahaemolyticus, unknown function, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2od0__assembly_1__model_1

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

Download this curve (.dat)

2od0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2od0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.24 Å
Rg (electron density)	19.06 Å
Total Rg	19.80 Å
Atom count	1687
Residues	199
Excluded volume	30220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2od0__assembly_1__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	Hypothetical protein VP1028
Molecular weight formula_weight	12149.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1895

MDKPILKDSMKLFEALGTIKSRSMFGGFGLFADETMFALVVNNQLHIRADQQTSSDFETQGLKPYVYKKRGFPVVTKYYAISSELWESSDRLIEVAKKSLENAKL

Source Source

Source organism organism	Vibrio parahaemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	223926
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

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	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2od0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.5 — YgaC/TfoX-N like
Family Family family	d.198.5.2 — TfoX N-terminal domain-like

Domain ID domain_id	d2od0b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.5 — YgaC/TfoX-N like
Family Family family	d.198.5.2 — TfoX N-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	2od0A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	30 — YgaC/TfoX-N like chaperone

Domain ID domain_id	2od0B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	30 — YgaC/TfoX-N like chaperone

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Unit-cell length a length_a	42.458 Å
Unit-cell length b length_b	42.876 Å
Unit-cell length c length_c	157.900 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	79.060 Å
R factor r_factor	0.2019
R_work r_work	0.1996
R_free r_free	0.2452

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

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

Hypothetical protein VP1028

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

2od0__assembly_1__model_1

2od0__assembly_1__model_1 | I(q)

2od0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

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

Hypothetical protein VP1028

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

2od0__assembly_1__model_1

2od0__assembly_1__model_1 | I(q)

2od0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)