4FC9 | pdb_00004fc9

Structure of the C-terminal domain of the type III effector Xcv3220 (XopL)

• PDB DOI: https://doi.org/10.2210/pdb4FC9/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-24 Released: 2012-06-13 
• Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Tan, K., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Structure of the C-terminal domain of the type III effector Xcv3220 (XopL)

Singer, A.U., Schulze, S., Xu, X., Skarina, T., Cui, H., Egler, M., Srikumar, T., Raught, B., Savchenko, A., Bonas, U.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.38 kDa 
• Atom Count: 4,543 
• Modeled Residue Count: 515 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A [auth B], B [auth A], C	208	Xanthomonas euvesicatoria pv. vesicatoria str. 85-10	Mutation(s): 0  Gene Names: XCV3220
UniProt
Find proteins for Q3BQL2 (Xanthomonas euvesicatoria pv. vesicatoria (strain 85-10)) Explore Q3BQL2  Go to UniProtKB:  Q3BQL2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B], F [auth B], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth B], G [auth A], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B], B [auth A], C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34FC9

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.198	α = 90
b = 119.198	β = 90
c = 38.679	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXCD	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Tan, K., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary