1Y1S

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Sulfate Ion at 2.55A Resolution

PDB DOI: https://doi.org/10.2210/pdb1Y1S/pdb

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

Deposited: 2004-11-19 Released: 2005-11-22
Deposition Author(s): Gabdoulkhakov, A.G., Dontsova, M.V., Kachalova, G.S., Betzel, C., Ealick, S.E., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.231
R-Value Work: 0.189
R-Value Observed: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structures of Salmonella Typhimurium Uridine Phosphorylase in Native and Three Complexes Forms - with Uridine, Uracil and Sulfate.

Gabdoulkhakov, A.G., Dontsova, M.V., Kachalova, G.S., Betzel, C., Ealick, S.E., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.15 kDa
Atom Count: 11,544
Modelled Residue Count: 1,500
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 [auth C] C [auth D] D [auth F] E A, B [auth C], C [auth D], D [auth F], E, F [auth B]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A1F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA Query on URA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth D] SDF format, chain M [auth F] SDF format, chain O [auth E] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth D] MOL2 format, chain M [auth F] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth D] mmCIF format, chain M [auth F] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth B]	H [auth A], K [auth D], M [auth F], O [auth E], Q [auth B]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth D] Focus chain M [auth F] Focus chain O [auth E] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth D] Focus chain M [auth F] Focus chain O [auth E] Focus chain Q [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain L [auth F] SDF format, chain N [auth E] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth F] MOL2 format, chain N [auth E] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth F] mmCIF format, chain N [auth E] mmCIF format, chain P [auth B]	G [auth A] I [auth C] J [auth D] L [auth F] N [auth E] G [auth A], I [auth C], J [auth D], L [auth F], N [auth E], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth F] Focus chain N [auth E] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth F] Focus chain N [auth E] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.231
R-Value Work: 0.189
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.99	α = 90
b = 124.12	β = 90
c = 133.83	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-11-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-04-03
Changes: Refinement description