3LJL | pdb_00003ljl

The crystal structure of the full-length transcriptional regulator LuxT from Vibrio parahaemolyticus RIMD 2210633.

• PDB DOI: https://doi.org/10.2210/pdb3LJL/pdb

• Classification: transcription regulator
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-01-26 Released: 2010-02-09 
• Deposition Author(s): Tan, K., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.261 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

The crystal structure of the full-length transcriptional regulator LuxT from Vibrio parahaemolyticus RIMD 2210633.

Tan, K., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.55 kDa 
• Atom Count: 2,396 
• Modeled Residue Count: 298 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator LuxT	A, B	156	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], D [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.261 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.792	α = 90
b = 89.792	β = 90
c = 125.028	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Tan, K., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary