4O2I | pdb_00004o2i

The crystal structure of non-LEE encoded type III effector C from Citrobacter rodentium

• PDB DOI: https://doi.org/10.2210/pdb4O2I/pdb

• Classification: HYDROLASE
• Organism(s): Citrobacter rodentium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-17 Released: 2014-01-15 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The crystal structure of non-LEE encoded type III effector C from Citrobacter rodentium

Chang, C., Xu, X., Cui, H., Savchenko, A., Adkins, J., Joachimiak, A.

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: 73.54 kDa 
• Atom Count: 4,063 
• Modeled Residue Count: 498 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-LEE encoded type III effector C	A, B	324	Citrobacter rodentium	Mutation(s): 0  Gene Names: nleC
UniProt
Find proteins for Q6RYA8 (Citrobacter rodentium) Explore Q6RYA8  Go to UniProtKB:  Q6RYA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.937	α = 90
b = 89.356	β = 90
c = 205.416	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-05-07
  Changes: Structure summary
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary