5TF3 | pdb_00005tf3

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)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2U2GWH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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: 2.00 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:

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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

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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.