5M2T | pdb_00005m2t

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

PDB DOI: https://doi.org/10.2210/pdb5M2T/pdb

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

Deposited: 2016-10-13 Released: 2017-11-15
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.
Funding Organization(s): RFBR, Grant of President of Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.137 (Depositor), 0.141 (DCC)
R-Value Work:
0.118 (Depositor), 0.121 (DCC)
R-Value Observed:
0.118 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdulkhakov, A.G., Dontsova, M.V., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.49 kDa
Atom Count: 14,855
Modeled Residue Count: 1,509
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K4U1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URI Query on URI Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] I [auth B] K [auth C] O [auth D] S [auth E] G [auth A], I [auth B], K [auth C], O [auth D], S [auth E], V [auth F]	URIDINE C₉ H₁₂ N₂ O₆ DRTQHJPVMGBUCF-XVFCMESISA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain V [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E] mmCIF format, chain U [auth E]	U [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain W [auth F] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain W [auth F] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain W [auth F]	J [auth B] L [auth C] M [auth C] P [auth D] Q [auth D] J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D], W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth F] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth C] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain T [auth E] mmCIF format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain T [auth E]	H [auth A], N [auth C], T [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth C] Focus chain T [auth E] Interactions & Density Focus chain H [auth A] Focus chain N [auth C] Focus chain T [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.137 (Depositor), 0.141 (DCC)
R-Value Work: 0.118 (Depositor), 0.121 (DCC)
R-Value Observed: 0.118 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.323	α = 110.56
b = 72.039	β = 107.53
c = 89.193	γ = 85.83

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952a
Grant of President of Russian Federation	Russian Federation	MK-9246.2016.3

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description