4I2V | pdb_00004i2v

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 2.12A resolution

PDB DOI: https://doi.org/10.2210/pdb4I2V/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-23 Released: 2013-12-18
Deposition Author(s): Lashkov, A.A., Balaev, V.V., Prokofev, I.I., Betzel, C., Gabdoulkhakov, A.G., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.242 (Depositor), 0.228 (DCC)
R-Value Work:
0.200 (Depositor), 0.202 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 2.12A resolution

Lashkov, A.A., Balaev, V.V., Prokofev, I.I., Betzel, C., Gabdoulkhakov, A.G., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 162.75 kDa
Atom Count: 11,322
Modeled Residue Count: 1,500
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Yersinia pseudotuberculosis	Mutation(s): 0 Gene Names: udp EC: 2.4.2.3
UniProt
Find proteins for Q7AZX0 (Yersinia pseudotuberculosis) Explore Q7AZX0 Go to UniProtKB: Q7AZX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7AZX0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.242 (Depositor), 0.228 (DCC)
R-Value Work: 0.200 (Depositor), 0.202 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.68	α = 90
b = 156.68	β = 90
c = 48.46	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Gabdoulkhakov, A.G.

Mikhailov, A.M.

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.