2QSX | pdb_00002qsx

Crystal structure of putative transcriptional regulator LysR From Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2QSX/pdb

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


• Deposited: 2007-07-31 Released: 2007-09-04 
• Deposition Author(s): Wu, R., Abdullah, J., Binkowski, T.A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

The Crystal Structure of Putative Transcriptional Regulator LysR From Vibrio parahaemolyticus.

Wu, R., Abdullah, J., Binkowski, T.A., 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: 50.38 kDa 
• Atom Count: 3,329 
• Modeled Residue Count: 365 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator, LysR family	A, B	218	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VP0635
UniProt
Find proteins for Q87RY9 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87RY9  Go to UniProtKB:  Q87RY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.64 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.291	α = 90
b = 83.11	β = 90
c = 95.509	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Wu, R., Abdullah, J., Binkowski, T.A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary