2HRD | pdb_00002hrd

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution

PDB DOI: https://doi.org/10.2210/pdb2HRD/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-07-20 Released: 2007-07-24
Deposition Author(s): Timofeev, V.I., Gabdulkhakov, A.G., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.188 (DCC)
R-Value Work:
0.166 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution

Timofeev, V.I., Gabdulkhakov, A.G., Mikhailov, A.M., Dontsova, M.V., Voelter, W., Betzel, C.

To be published.

Macromolecule Content

Total Structure Weight: 165.23 kDa
Atom Count: 12,584
Modeled Residue Count: 1,483
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: 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
TDR Query on TDR Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Y [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] P [auth C] S [auth D] U [auth E] I [auth A], L [auth B], P [auth C], S [auth D], U [auth E], Y [auth F]	THYMINE C₅ H₆ N₂ O₂ RWQNBRDOKXIBIV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain Y [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	G [auth A] H [auth A] K [auth B] O [auth C] R [auth D] G [auth A], H [auth A], K [auth B], O [auth C], R [auth D], T [auth E], W [auth F], X [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B], Q [auth C], V [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.189 (Depositor), 0.188 (DCC)
R-Value Work: 0.166 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.2	α = 90
b = 123.4	β = 90
c = 133.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Timofeev, V.I.

Gabdulkhakov, A.G.

Mikhailov, A.M.

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description