3OXN | pdb_00003oxn

The crystal structure of a putative transcriptional regulator from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb3OXN/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-09-21 Released: 2010-10-13
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.290 (Depositor), 0.315 (DCC)
R-Value Work:
0.245 (Depositor)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3OXN

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of a putative transcriptional regulator from Vibrio parahaemolyticus

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 111.34 kDa
Atom Count: 6,886
Modeled Residue Count: 853
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator, LysR family	A, B, C, D	241	Vibrio parahaemolyticus	Mutation(s): 0 Gene Names: VP0027
UniProt
Find proteins for Q87TP2 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87TP2 Go to UniProtKB: Q87TP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87TP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.290 (Depositor), 0.315 (DCC)
R-Value Work: 0.245 (Depositor)
R-Value Observed: 0.248 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.316	α = 86.19
b = 50.488	β = 82.89
c = 108.116	γ = 86.74

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary

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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.