SAXSdb — 1vmf

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

hypothetical protein

Bacillus halodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 1 ACETATE ION × 2 1,2-ETHANEDIOL × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K772_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–145； UniProt 1–133 Author chain B； PDBConstruct 13–145； UniProt 1–133 Author chain C； PDBConstruct 13–145； UniProt 1–133

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	1vmf
Deposition date deposition_date	2004-09-23
Structure title title	CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION
Keywords keywords	STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, UNKNOWN FUNCTION; 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.

1vmf__assembly_1__model_1

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

Download this curve (.dat)

1vmf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vmf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.14 Å
Rg (electron density)	19.78 Å
Total Rg	20.63 Å
Atom count	3261
Residues	407
Excluded volume	57395 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vmf__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	hypothetical protein
Molecular weight formula_weight	16563.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3727

MGSDKIHHHHHHMKTFHLTTQSRDEMVDITSQIETWIRETGVTNGVAIVSSLHTTAGITVNENADPDVKRDMIMRLDEVYPWHHENDRHMEGNTAAHLKTSTVGHAQTLIISEGRLVLGTWQGVYFCEFDGPRTNRKFVVKLLTD

Source Source

Source organism organism	Bacillus halodurans
NCBI taxonomy ID ncbi_taxonomy_id	86665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	417

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1vmfa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.273 — YjbQ-like
Superfamily Superfamily superfamily	d.273.1 — YjbQ-like
Family Family family	d.273.1.1 — YjbQ-like

Domain ID domain_id	d1vmfa2
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	d1vmfb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.273 — YjbQ-like
Superfamily Superfamily superfamily	d.273.1 — YjbQ-like
Family Family family	d.273.1.1 — YjbQ-like

Domain ID domain_id	d1vmfb2
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	d1vmfc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.273 — YjbQ-like
Superfamily Superfamily superfamily	d.273.1 — YjbQ-like
Family Family family	d.273.1.1 — YjbQ-like

Domain ID domain_id	d1vmfc2
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	1vmfA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	460 — YjbQ-like

Domain ID domain_id	1vmfB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	460 — YjbQ-like

Domain ID domain_id	1vmfC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	460 — YjbQ-like

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Unit-cell length a length_a	57.601 Å
Unit-cell length b length_b	58.951 Å
Unit-cell length c length_c	134.964 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	12

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

Resolution resolution	1.460 Å
Low-resolution limit resolution_low	29.480 Å
R factor r_factor	0.1496
R_work r_work	0.1483
R_free r_free	0.1748

CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION

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

hypothetical 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

1vmf__assembly_1__model_1

1vmf__assembly_1__model_1 | I(q)

1vmf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION

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

hypothetical 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

1vmf__assembly_1__model_1

1vmf__assembly_1__model_1 | I(q)

1vmf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)