SAXSdb — 1xmx

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

hypothetical protein VC1899

Vibrio cholerae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GLYCEROL × 2 FORMIC ACID × 6 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 GLYCEROL × 4 FORMIC ACID × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KQU9_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–385； UniProt 1–383

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	1xmx
Deposition date deposition_date	2004-10-04
Structure title title	Crystal structure of protein VC1899 from Vibrio cholerae
Keywords keywords	alpha-beta, MCSG, protein structure initiative, Structural Genomics, PSI, Midwest Center for Structural Genomics, 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.

1xmx__assembly_1__model_1

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

Download this curve (.dat)

1xmx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xmx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.96 Å
Rg (electron density)	25.50 Å
Total Rg	26.08 Å
Atom count	3067
Residues	380
Excluded volume	54315 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xmx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xmx__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	hypothetical protein VC1899
Molecular weight formula_weight	43825.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3463

NAMAIHVGIIDQDPVRLVTPLLDHRTVSRHIIFIGDHTQTVIYQRLSDVLNKRNISTDFFEIPAGSNTSAIKSAIRELAETLKARGEEVKFNASCGLRHRLLSAYEVFRSYHWPIFVVEPNSDCLCWLYPEGNNDTQVQDRITIADYLTIFGARGEFNEHQLSPQLDQQLYQLGERWASNALELGPGLATLNYLATTCRKEQKLDVELSDKQQGYRELNLLLSDLVEAKIASYENGILTFINEEARRFANGEWLETLVHSTVKQIQDDMPTIQDRSLNVQVYRQLGEREVRNELDVATVVNNKLHIIECKTKGMRDDGDDTLYKLESLRDLLGGLQARAMLVSFRPLRHNDITRAEDLGLALIGPDELKDLKTHLTQWFKAAGGN

Source Source

Source organism organism	Vibrio cholerae
NCBI taxonomy ID ncbi_taxonomy_id	666
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	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	396

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xmxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.26 — Hypothetical protein VC1899

Domain ID domain_id	d1xmxa2
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 (3 domains)

Domain ID domain_id	1xmxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10770 — Hypothetical protein VC1899 like domain (Restriction endonuclease-like)

Domain ID domain_id	1xmxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1xmxA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	680 — Hypothetical protein VC1899 (Restriction endonuclease-like)

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Unit-cell length a length_a	66.549 Å
Unit-cell length b length_b	71.439 Å
Unit-cell length c length_c	90.096 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	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1726
R_work r_work	0.1684
R_free r_free	0.2537

Crystal structure of protein VC1899 from Vibrio cholerae

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

hypothetical protein VC1899

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

1xmx__assembly_1__model_1

1xmx__assembly_1__model_1 | I(q)

1xmx__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of protein VC1899 from Vibrio cholerae

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

hypothetical protein VC1899

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

1xmx__assembly_1__model_1

1xmx__assembly_1__model_1 | I(q)

1xmx__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)