4H43 | pdb_00004h43

Structure of the Salmonella plasmid virulence C protein (SpvC) H106N mutant.

• PDB DOI: https://doi.org/10.2210/pdb4H43/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-09-16 Released: 2013-08-07 
• Deposition Author(s): Shenoy, A.G., Johnson, S.J., Hengge, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structural and mechanistic Investigations of phosphothreonine lyase class of enzymes.

Shenoy, A.G., Kuznetsov, V., 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: 55.31 kDa 
• Atom Count: 3,669 
• Modeled Residue Count: 428 
• 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): 1  Gene Names: mkaD, PSLT038, salmonella plasmid virulence (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: 2.30 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.989	α = 90
b = 70.989	β = 90
c = 142.972	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Shenoy, A.G., Johnson, S.J., Hengge, A.C.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description