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)

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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 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LuxT	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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	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

Entry History 

Deposition Data

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

Revision History  

• 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