4NY1 | pdb_00004ny1

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 (Depositor), 0.194 (DCC)
R-Value Work:
0.162 (Depositor), 0.164 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4NY1

This is version 1.1 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.

Macromolecule Content

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

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3NID1
Sequence Annotations 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] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
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] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.162 (Depositor), 0.164 (DCC)
R-Value Observed: 0.163 (Depositor)

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

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View more in-depth experimental data

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
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.