4OGK | pdb_00004ogk

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb4OGK/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-16 Released: 2015-03-04
Deposition Author(s): Sotnichenko, S.E., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.223 (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 the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

Sotnichenko, S.E., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.87 kDa
Atom Count: 11,404
Modeled Residue Count: 1,495
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	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: STM3968, STMD1.21, udp EC: 2.4.2.3
UniProt
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1F6 Go to UniProtKB: P0A1F6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A1F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 J [auth B] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain Q [auth F]	G [auth A], J [auth B], L [auth D], N [auth E], Q [auth F]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth E] Focus chain Q [auth F]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E] mmCIF format, chain O [auth E]	O [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain S [auth F] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth E] MOL2 format, chain S [auth F] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain P [auth E] mmCIF format, chain S [auth F] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], P [auth E], S [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain P [auth E] Focus chain S [auth F]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.220 (Depositor)
R-Value Observed: 0.223 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.97	α = 90
b = 89.97	β = 90
c = 256.56	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description