SAXSdb — 3ck6

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

Putative membrane transport protein

Vibrio parahaemolyticus RIMD 2210633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	CHLORIDE ION × 25 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87M69_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–252； UniProt 1–249 Author chain B； PDBConstruct 4–252； UniProt 1–249 Author chain C； PDBConstruct 4–252； UniProt 1–249 Author chain D； PDBConstruct 4–252； UniProt 1–249 Author chain E； PDBConstruct 4–252； UniProt 1–249

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	3ck6
Deposition date deposition_date	2008-03-14
Structure title title	Crystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633
Keywords keywords	;APC91421.1, ZntB, cytoplasmic domain, Vibrio parahaemolyticus RIMD 2210633, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
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.

3ck6__assembly_1__model_1

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

Download this curve (.dat)

3ck6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ck6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.06 Å
Rg (electron density)	33.82 Å
Total Rg	34.50 Å
Atom count	10033
Residues	1185
Excluded volume	177170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ck6__assembly_1__model_1`	pentameric （5）	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 (3)

Entity 1 Entity 1 polymer

Description description	Putative membrane transport protein
Molecular weight formula_weight	29629.1 kDa
Mutation mutation	S42G
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	10739

SNAMGFMIEHWDFSTPMATQETTTAEHIQPNHWYHCERLHPDIRGWLEDNHVPRATVDHLLADESRPSFHPLDDDNFMLILRGINMNENASPEDMLSIRILYFQGALISTRKIPSRAIMEIRQALAEHKGPKSLASLLNQIIEGLNGKIDLYLDTIEETLNEFDVNDESTYNHIAAQKALISIKRFIRPQQYAIRDLIESESELVTSRPHQYRFAHNNITRINETIEFYLGEVALFQDEIKHNRDEKTNKNS

Source Source

Source organism organism	Vibrio parahaemolyticus RIMD 2210633
NCBI taxonomy ID ncbi_taxonomy_id	223926
Host organism host_organism	Escherichia coli BL21

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	25

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	670

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3ck6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	20 — CorA soluble domain-like

Domain ID domain_id	3ck6A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	340 — Magnesium transport protein CorA, transmembrane region

Domain ID domain_id	3ck6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	20 — CorA soluble domain-like

Domain ID domain_id	3ck6B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	340 — Magnesium transport protein CorA, transmembrane region

Domain ID domain_id	3ck6C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	20 — CorA soluble domain-like

Domain ID domain_id	3ck6C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	340 — Magnesium transport protein CorA, transmembrane region

Domain ID domain_id	3ck6D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	20 — CorA soluble domain-like

Domain ID domain_id	3ck6D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	340 — Magnesium transport protein CorA, transmembrane region

Domain ID domain_id	3ck6E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	20 — CorA soluble domain-like

Domain ID domain_id	3ck6E02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	340 — Magnesium transport protein CorA, transmembrane region

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Unit-cell length a length_a	64.390 Å
Unit-cell length b length_b	130.213 Å
Unit-cell length c length_c	79.386 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.800 Å
R factor r_factor	0.1869
R_work r_work	0.1849
R_free r_free	0.2235

Crystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633

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

Putative membrane transport 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

3ck6__assembly_1__model_1

3ck6__assembly_1__model_1 | I(q)

3ck6__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633

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

Putative membrane transport 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

3ck6__assembly_1__model_1

3ck6__assembly_1__model_1 | I(q)

3ck6__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)