3KUX | pdb_00003kux

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 (CSGID)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 38.76 kDa
Atom Count: 2,750
Modeled Residue Count: 349
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S9PM40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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:

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

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Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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
Version 1.5: 2025-10-22
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.