3BO6

Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector protein

• PDB DOI: https://doi.org/10.2210/pdb3BO6/pdb

• Classification: LYASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-17 Released: 2008-11-25 
• Deposition Author(s): Brennan, D.F., Roe, S.M., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.189 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Literature

Structure and Mechanism of the Chromobacterium violaceum VirA Phosphothreonine Lyase Type III Secretion System Effector

Brennan, D.F., Roe, S.M., Barford, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.57 kDa 
• Atom Count: 4,304 
• Modelled Residue Count: 435 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrophilic protein, virA protein	A, B	220	Chromobacterium violaceum	Mutation(s): 0  Gene Names: spvC EC: 4.2.3
UniProt
Find proteins for Q7NYG6 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NYG6  Go to UniProtKB:  Q7NYG6

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.189 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.671	α = 90
b = 119.777	β = 105.63
c = 44.492	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Brennan, D.F., Roe, S.M., Barford, D.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations