1Y1T

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium at 1.77A Resolution

PDB DOI: https://doi.org/10.2210/pdb1Y1T/pdb

Classification: TRANSCRIPTION
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: 1.77 Å
R-Value Free: 0.205
R-Value Work: 0.184
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 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: 54.53 kDa
Atom Count: 3,773
Modelled Residue Count: 468
Deposited Residue Count: 506
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 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% 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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth F] MOL2 format, chain D [auth F] mmCIF format, chain D [auth F]	D [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth F] Interactions & Density Focus chain D [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.205
R-Value Work: 0.184
R-Value Observed: 0.184
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.82	α = 90
b = 150.82	β = 90
c = 47.84	γ = 120

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: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

1Y1T

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium at 1.77A Resolution

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)