Macromolecule Content

Total Structure Weight: 54.63 kDa
Atom Count: 4,356
Modelled Residue Count: 502
Deposited Residue Count: 506
Unique protein chains: 1

4NY1

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.7 A resolution

PDB DOI: https://doi.org/10.2210/pdb4NY1/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis IP 32953
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-10 Released: 2015-01-07
Deposition Author(s): Balaev, V.V., Gabdoulkhakov, A.G., Lashkov, A.A., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.7 A resolution

Balaev, V.V., Gabdoulkhakov, A.G., Lashkov, A.A., Mikhailov, A.M.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B	253	Yersinia pseudotuberculosis IP 32953	Mutation(s): 0 Gene Names: udp, YPTB0250 EC: 2.4.2.3
UniProt
Find proteins for I3NID1 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore I3NID1 Go to UniProtKB: I3NID1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3NID1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	D [auth A], E [auth A], F [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.742	α = 90
b = 150.742	β = 90
c = 46.31	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-01-07

Deposition Author(s):

Gabdoulkhakov, A.G.

Mikhailov, A.M.

Revision History (Full details and data files)

Version 1.0: 2015-01-07
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.