5TF3

Crystal Structure of Protein of Unknown Function YPO2564 from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb5TF3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-23 Released: 2016-10-19 
• Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Anderson, W.F., Crosson, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal Structure of Protein of Unknown Function YPO2564 from Yersinia pestis

Kim, Y., Chhor, G., Endres, M., Babnigg, G., Anderson, W.F., Crosson, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content

• Total Structure Weight: 15.32 kDa 
• Atom Count: 1,208 
• Modelled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein	A	131	Yersinia pestis CO92	Mutation(s): 0
UniProt
Find proteins for A0A2U2GWH2 (Yersinia pestis) Explore A0A2U2GWH2  Go to UniProtKB:  A0A2U2GWH2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35tf3

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.094	α = 90
b = 75.094	β = 90
c = 73.772	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Anderson, W.F., Crosson, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary