4npa

Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup

Method: X-RAY DIFFRACTION

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

Putative uncharacterized protein

Vibrio cholerae O1 biovar El Tor

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 1 PHOSPHATE ION × 3 DI(HYDROXYETHYL)ETHER × 1 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	4npa
Deposition date deposition_date	2013-11-21
Structure title title	Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup
Keywords keywords	unknown function, 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.

4npa__assembly_1__model_1

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

Download this curve (.dat)

4npa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4npa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.10 Å
Rg (electron density)	37.30 Å
Total Rg	37.66 Å
Atom count	12563
Residues	1669
Excluded volume	222860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4npa__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	50893.3 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	12881

MSLIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIVTEG

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	301

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d4npaa1
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	d4npaa2
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	d4npaa3
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	d4npaa4
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	d4npab1
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	d4npab2
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	d4npab3
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	d4npab4
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	d4npac1
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	d4npac2
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	d4npac3
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	d4npac4
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	d4npad1
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	d4npad2
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	d4npad3
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	d4npad4
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	4npaA01
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	4npaA02
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	4npaB01
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	4npaB02
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	4npaC01
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	4npaC02
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	4npaD01
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	4npaD02
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	58.330 Å
Unit-cell length b length_b	96.340 Å
Unit-cell length c length_c	333.260 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	16

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.740 Å
R factor r_factor	0.2094
R_work r_work	0.2064
R_free r_free	0.2667

Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup

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

Putative uncharacterized 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

4npa__assembly_1__model_1

4npa__assembly_1__model_1 | I(q)

4npa__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup

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

Putative uncharacterized 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

4npa__assembly_1__model_1

4npa__assembly_1__model_1 | I(q)

4npa__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)