SAXSdb — 1vpb

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

putative modulator of DNA gyrase

Bacteroides thetaiotaomicron

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A1L2_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–451； UniProt 1–439

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	1vpb
Deposition date deposition_date	2004-10-15
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION
Keywords keywords	;PUTATIVE MODULATOR OF DNA GYRASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, HYDROLASE ;; HYDROLASE
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.

1vpb__assembly_1__model_1

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

Download this curve (.dat)

1vpb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vpb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.32 Å
Rg (electron density)	29.28 Å
Total Rg	30.18 Å
Atom count	6674
Residues	874
Excluded volume	118600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vpb__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	putative modulator of DNA gyrase
Molecular weight formula_weight	49845.0 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	3863

MGSDKIHHHHHHMITDENKKLAQWAMDYALKNGCQAAKVLLYSSSNTSFELRDAKMDRLQQASEGGLSLSLYVDGRYGSISTNRLNRKELETFIKNGIDSTRYLAKDEARVLADPSRYYKGGKPDLKLYDAKFASLNPDDKIEMAKAVAEEALGKDERIISVGSSYGDGEDFAYRLISNGFEGETKSTWYSLSADITIRGEGEARPSAYWYESSLYMNDLIKKGIGQKALERVLRKLGQKKVQSGKYTMVVDPMNSSRLLSPMISALNGSALQQKNSFLLNKLNEKIASDRLTLTDEPHLVKASGARYFDNEGIATERRSIFDKGVLNTYFIDTYNAKKMGVDPTISGSSILVMETGDKNLDGLIAGVEKGILVTGFNGGNNNSSTGDFSYGIEGFLIENGKLTQPVSEMNVTGNLITLWNSLVATGNDPRLNSSWRIPSLVFEGVDFSGL

Source Source

Source organism organism	Bacteroides thetaiotaomicron
NCBI taxonomy ID ncbi_taxonomy_id	226186
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	378

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vpba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.283 — Putative modulator of DNA gyrase, PmbA/TldD
Superfamily Superfamily superfamily	d.283.1 — Putative modulator of DNA gyrase, PmbA/TldD
Family Family family	d.283.1.1 — Putative modulator of DNA gyrase, PmbA/TldD

CATH v4.4 (1 domains)

Domain ID domain_id	1vpbA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2290 — PmbA/TldD fold
Homologous superfamily homologous superfamily	10 — PmbA/TldD superfamily

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Unit-cell length a length_a	73.541 Å
Unit-cell length b length_b	154.968 Å
Unit-cell length c length_c	106.120 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	43.780 Å
R factor r_factor	0.1795
R_work r_work	0.1782
R_free r_free	0.2039

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION

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

putative modulator of DNA gyrase

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

1vpb__assembly_1__model_1

1vpb__assembly_1__model_1 | I(q)

1vpb__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION

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

putative modulator of DNA gyrase

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

1vpb__assembly_1__model_1

1vpb__assembly_1__model_1 | I(q)

1vpb__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)