6EYP

X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A

PDB DOI: https://doi.org/10.2210/pdb6EYP/pdb

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

Deposited: 2017-11-13 Released: 2018-11-21
Deposition Author(s): Prokofev, I.I., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.
Funding Organization(s): Grant of the President of Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.170
R-Value Work: 0.138
R-Value Observed: 0.138

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A

Prokofev, I.I., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 163.48 kDa
Atom Count: 14,636
Modelled Residue Count: 1,508
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, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055... udp, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain I [auth B] SDF format, chain N [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E]	G [auth A] I [auth B] J [auth C] M [auth D] N [auth D] G [auth A], I [auth B], J [auth C], M [auth D], N [auth D], O [auth E], Q [auth F], R [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain P [auth E] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain P [auth E] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain P [auth E]	H [auth A], K [auth C], P [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain P [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.170
R-Value Work: 0.138
R-Value Observed: 0.138
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.94	α = 90
b = 92.94	β = 90
c = 140.231	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Grant of the President of Russian Federation	Russian Federation	MK-9246.2016.3.

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description