1VPB | pdb_00001vpb

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

PDB DOI: https://doi.org/10.2210/pdb1VPB/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-10-15 Released: 2004-11-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.180 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative modulator of DNA gyrase (bt3649) from Bacteroides thetaiotaomicron vpi-5482 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 49.97 kDa
Atom Count: 3,863
Modeled Residue Count: 437
Deposited Residue Count: 451
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative modulator of DNA gyrase	A	451	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: bt3649
UniProt
Find proteins for Q8A1L2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A1L2 Go to UniProtKB: Q8A1L2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A1L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.541	α = 90
b = 154.968	β = 90
c = 106.12	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-11-09

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-11-09
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-05-22
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.