3B4S

Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633

PDB DOI: https://doi.org/10.2210/pdb3B4S/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-10-24 Released: 2007-11-06
Deposition Author(s): Tan, K., Zhou, M., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633.

Tan, K., Zhou, M., Gu, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 87.34 kDa
Atom Count: 5,906
Modelled Residue Count: 727
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LuxT	A, B, C, D, E A, B, C, D, E, F, G, H	94	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VPA0420
UniProt
Find proteins for Q87J33 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87J33 Go to UniProtKB: Q87J33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87J33
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.438	α = 90
b = 147.438	β = 90
c = 382.487	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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 R01GM133198.