3D8U

The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633

PDB DOI: https://doi.org/10.2210/pdb3D8U/pdb

Classification: transcription regulator
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-23 Released: 2008-07-22
Deposition Author(s): Tan, K., Hatzos, C., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.283 (Depositor), 0.285 (DCC)
R-Value Work:
0.214 (Depositor), 0.212 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633

Tan, K., Hatzos, C., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 61.05 kDa
Atom Count: 3,935
Modelled Residue Count: 534
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PurR transcriptional regulator	A, B	275	Vibrio parahaemolyticus	Mutation(s): 0 Gene Names: VPA0232
UniProt
Find proteins for Q87JL7 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87JL7 Go to UniProtKB: Q87JL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87JL7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.283 (Depositor), 0.285 (DCC)
R-Value Work: 0.214 (Depositor), 0.212 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.264	α = 90
b = 126.264	β = 90
c = 83.76	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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.