4HAH | pdb_00004hah

Structure of the Salmonella plasmid virulence C protein (SpvC)

• PDB DOI: https://doi.org/10.2210/pdb4HAH/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-09-26 Released: 2013-10-02 
• Deposition Author(s): Shenoy, A.G., Johnson, S.J., Hengge, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Mechanistic and structural investigations of phosphothreonine lyase class of enzymes.

Vyacheslav, I.K., Shenoy, A.G., Johnson, S.J., Hengge, A.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.36 kDa 
• Atom Count: 3,964 
• Modeled Residue Count: 430 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
27.5 kDa virulence protein	A, B	241	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: mkaD, PSLT038, SPV, spvC, vsdD EC: 4.2.3
UniProt
Find proteins for P0A2M9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2M9  Go to UniProtKB:  P0A2M9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.528	α = 90
b = 71.912	β = 90
c = 106.49	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Shenoy, A.G., Johnson, S.J., Hengge, A.C.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references