3KUX

Structure of the YPO2259 putative oxidoreductase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3KUX/pdb

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


• Deposited: 2009-11-28 Released: 2009-12-22 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Gordon, E., Kwon, K., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases, Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Structure of the YPO2259 putative oxidoreductase from Yersinia pestis

Anderson, S.M., Wawrzak, Z., Gordon, E., Kwon, K., Edwards, A., Savchenko, A., Anderson, W.F., 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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

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: 38.76 kDa 
• Atom Count: 2,750 
• Modelled Residue Count: 349 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A	352	Yersinia pestis	Mutation(s): 0  Gene Names: mviM4, y2101, YPO2259, YP_2055
UniProt
Find proteins for A0A2S9PM40 (Yersinia pestis) Explore A0A2S9PM40  Go to UniProtKB:  A0A2S9PM40

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.75 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33kux

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.55	α = 90
b = 97.55	β = 90
c = 172.51	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Gordon, E., Kwon, K., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-12-14
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary