3DPS | pdb_00003dps

X-ray structure of the unliganded uridine phosphorylase from salmonella typhimurium in homodimeric form at 1.8A

PDB DOI: https://doi.org/10.2210/pdb3DPS/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-09 Released: 2009-07-14
Deposition Author(s): Mikhailov, A.M., Lashkov, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.197 (DCC)
R-Value Work:
0.161 (Depositor), 0.157 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3DPS

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

Literature

X-ray structure of the unliganded uridine phosphorylase from salmonella typhimurium in homodimeric form at 1.8A

Lashkov, A.A., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 54.43 kDa
Atom Count: 3,821
Modeled Residue Count: 476
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B [auth F]	253	Salmonella enterica subsp. enterica serovar Typhimurium	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth F] MOL2 format, chain C [auth F] mmCIF format, chain C [auth F]	C [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth F] Interactions & Density Focus chain C [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.200 (Depositor), 0.197 (DCC)
R-Value Work: 0.161 (Depositor), 0.157 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.86	α = 90
b = 150.86	β = 90
c = 47.84	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
EMBL	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Mikhailov, A.M.

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.