2QDK | pdb_00002qdk

X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium at 1.62A resolution

PDB DOI: https://doi.org/10.2210/pdb2QDK/pdb

Classification: TRANSFERASE
Organism(s): Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-06-21 Released: 2008-07-01
Deposition Author(s): Timofeev, V.I., Pavlyuk, B.P., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.235 (DCC)
R-Value Work:
0.191 (Depositor), 0.184 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 2QDK

This is version 1.2 of the entry. See complete history.

Literature

X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium at 1.62A resolution

Timofeev, V.I., Pavlyuk, B.P., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 162.23 kDa
Atom Count: 12,851
Modeled Residue Count: 1,467
Deposited Residue Count: 1,512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	252	N/A	Mutation(s): 0 Gene Names: udp EC: 2.4.2.3
UniProt
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1F6 Go to UniProtKB: P0A1F6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A1F6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.235 (DCC)
R-Value Work: 0.191 (Depositor), 0.184 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.6	α = 90
b = 125.03	β = 90
c = 134.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-07-01

Deposition Author(s):

Gabdoulkhakov, A.G.

Mikhailov, A.M.

Revision History (Full details and data files)

Version 1.0: 2008-07-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references

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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.