4IP0

X-Ray Structure of the Complex Uridine Phosphorylase from Vibrio cholerae with Phosphate Ion at 1.29 A Resolution

PDB DOI: https://doi.org/10.2210/pdb4IP0/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-09 Released: 2014-08-13
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.200
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Seregina, T.A., Mironov, A.S., Betzel, C., Mikhailov, A.M.

(2016) Crystallogr Rep 61: 954-973

DOI: https://doi.org/10.1134/S1063774516060134

Macromolecule Content

Total Structure Weight: 164.25 kDa
Atom Count: 13,706
Modelled Residue Count: 1,505
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0 Gene Names: udp EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1 Go to UniProtKB: Q9K4U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K4U1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E]	K [auth B], L [auth B], T [auth D], V [auth E], W [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	I [auth B], J [auth B], O [auth C], Y [auth F], Z [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth C] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth C] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain X [auth E] MOL2 format, chain M [auth B] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain X [auth E] mmCIF format, chain M [auth B] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain X [auth E]	BA [auth F] CA [auth F] H [auth A] M [auth B] Q [auth C] BA [auth F], CA [auth F], H [auth A], M [auth B], Q [auth C], R [auth C], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain X [auth E]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain P [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain P [auth C] mmCIF format, chain AA [auth F] mmCIF format, chain P [auth C]	AA [auth F], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain P [auth C] Interactions & Density Focus chain AA [auth F] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth E] MOL2 format, chain G [auth A] MOL2 format, chain U [auth E] mmCIF format, chain G [auth A] mmCIF format, chain U [auth E]	G [auth A], U [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain U [auth E] Interactions & Density Focus chain G [auth A] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.200
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.671	α = 69.63
b = 71.062	β = 72.56
c = 87.908	γ = 85.73

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations