3V4H

Crystal structure of a type VI secretion system effector from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3V4H/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-14 Released: 2011-12-28 
• Deposition Author(s): Filippova, E.V., Halavaty, A., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

Crystal structure of a type VI secretion system effector from Yersinia pestis

Filippova, E.V., Halavaty, A., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.39 kDa 
• Atom Count: 2,126 
• Modelled Residue Count: 260 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	185	Yersinia pestis	Mutation(s): 0  Gene Names: y1547, YPO2937, YP_2759
UniProt
Find proteins for Q8CLE0 (Yersinia pestis) Explore Q8CLE0  Go to UniProtKB:  Q8CLE0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: H 3 2
• Diffraction Data: https://doi.org/10.18430/m33v4h

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.55	α = 90
b = 148.55	β = 90
c = 82.573	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Filippova, E.V., Halavaty, A., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description