4G8J | pdb_00004g8j

X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine at 2.12 A Resolution

PDB DOI: https://doi.org/10.2210/pdb4G8J/pdb

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

Deposited: 2012-07-23 Released: 2013-07-24
Deposition Author(s): Lashkov, A.A., Gabdoulkhakov, A.G., Prokofev, I.I., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (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 phosphorylease from Vibrio cholerae complexed with thymidine

Lashkov, A.A., Gabdoulkhakov, A.G., Prokofev, I.I., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.79 kDa
Atom Count: 12,764
Modeled Residue Count: 1,496
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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(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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THM Query on THM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain Z [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F]	G [auth A] K [auth B] N [auth C] T [auth D] V [auth E] G [auth A], K [auth B], N [auth C], T [auth D], V [auth E], Z [auth F]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain W [auth E] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth E] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth E]	O [auth C], P [auth C], Q [auth C], W [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E] Interactions & Density Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain H [auth A] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain H [auth A]	AA [auth F] BA [auth F] CA [auth F] H [auth A] I [auth A] AA [auth F], BA [auth F], CA [auth F], H [auth A], I [auth A], L [auth B], R [auth C], U [auth D], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain J [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain J [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain J [auth A]	DA [auth F], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain J [auth A] Interactions & Density Focus chain DA [auth F] Focus chain J [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain Y [auth E] SDF format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain M [auth B]	M [auth B], S [auth C], Y [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth E] Interactions & Density Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.796	α = 90
b = 95.905	β = 119.96
c = 91.89	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description