3gh1

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

Method: X-RAY DIFFRACTION

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

Predicted nucleotide-binding protein

Vibrio cholerae O1 biovar El Tor str. N16961

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KTK3_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–454； UniProt 7–457 Author chain B； PDBConstruct 4–454； UniProt 7–457 Author chain C； PDBConstruct 4–454； UniProt 7–457 Author chain D； PDBConstruct 4–454； UniProt 7–457

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	3gh1
Deposition date deposition_date	2009-03-02
Structure title title	Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae
Keywords keywords	;STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, PSI, UNKNOWN FUNCTION, New York SGX Research Center for Structural Genomics ;; 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.

3gh1__assembly_1__model_1

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

Download this curve (.dat)

3gh1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gh1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.69 Å
Rg (electron density)	38.93 Å
Total Rg	39.23 Å
Atom count	13977
Residues	1711
Excluded volume	249750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gh1__assembly_1__model_1`	tetrameric （4）	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	Predicted nucleotide-binding protein
Molecular weight formula_weight	52566.2 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	15320

MSLIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIVTEGHHHHHH

Source Source

Source organism organism	Vibrio cholerae O1 biovar El Tor str. N16961
NCBI taxonomy ID ncbi_taxonomy_id	243277
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1329

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3gh1a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.65 — DUF4478 domain-like
Family Family family	d.58.65.1 — DUF4478 domain

Domain ID domain_id	d3gh1a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d3gh1a3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.68 — Anoctamin (TMEM16)-like
Superfamily Superfamily superfamily	f.68.2 — DUF3412 domain
Family Family family	f.68.2.1 — DUF3412 domain

Domain ID domain_id	d3gh1a4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gh1b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.65 — DUF4478 domain-like
Family Family family	d.58.65.1 — DUF4478 domain

Domain ID domain_id	d3gh1b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d3gh1b3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.68 — Anoctamin (TMEM16)-like
Superfamily Superfamily superfamily	f.68.2 — DUF3412 domain
Family Family family	f.68.2.1 — DUF3412 domain

Domain ID domain_id	d3gh1b4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gh1c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.65 — DUF4478 domain-like
Family Family family	d.58.65.1 — DUF4478 domain

Domain ID domain_id	d3gh1c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d3gh1c3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.68 — Anoctamin (TMEM16)-like
Superfamily Superfamily superfamily	f.68.2 — DUF3412 domain
Family Family family	f.68.2.1 — DUF3412 domain

Domain ID domain_id	d3gh1c4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gh1d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.65 — DUF4478 domain-like
Family Family family	d.58.65.1 — DUF4478 domain

Domain ID domain_id	d3gh1d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.129 — MCP/YpsA-like
Superfamily Superfamily superfamily	c.129.1 — MCP/YpsA-like
Family Family family	c.129.1.1 — MoCo carrier protein-like

Domain ID domain_id	d3gh1d3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.68 — Anoctamin (TMEM16)-like
Superfamily Superfamily superfamily	f.68.2 — DUF3412 domain
Family Family family	f.68.2.1 — DUF3412 domain

Domain ID domain_id	d3gh1d4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	3gh1A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1850 — MCP/YpsA-like
Homologous superfamily homologous superfamily	10 — MoCo carrier protein-like

Domain ID domain_id	3gh1A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3gh1B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1850 — MCP/YpsA-like
Homologous superfamily homologous superfamily	10 — MoCo carrier protein-like

Domain ID domain_id	3gh1B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3gh1C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1850 — MCP/YpsA-like
Homologous superfamily homologous superfamily	10 — MoCo carrier protein-like

Domain ID domain_id	3gh1C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3gh1D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1850 — MCP/YpsA-like
Homologous superfamily homologous superfamily	10 — MoCo carrier protein-like

Domain ID domain_id	3gh1D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

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Unit-cell length a length_a	59.034 Å
Unit-cell length b length_b	181.546 Å
Unit-cell length c length_c	95.772 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.32 °
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	1.900 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.1720
R_work r_work	0.1690
R_free r_free	0.2260

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

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

Predicted nucleotide-binding 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

3gh1__assembly_1__model_1

3gh1__assembly_1__model_1 | I(q)

3gh1__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

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

Predicted nucleotide-binding 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

3gh1__assembly_1__model_1

3gh1__assembly_1__model_1 | I(q)

3gh1__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)