3B4S | pdb_00003b4s

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 (Depositor), 0.232 (DCC)
R-Value Work:
0.190 (Depositor), 0.188 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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
Modeled Residue Count: 727
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 (Depositor), 0.232 (DCC)
R-Value Work: 0.190 (Depositor), 0.188 (DCC)
R-Value Observed: 0.192 (Depositor)

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
Version 1.2: 2024-10-16
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.