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- PDB-2rj3: Crystal Structure of the Uridine Phosphorylase from Salmonella Ty... -

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Basic information

Entry
Database: PDB / ID: 2rj3
TitleCrystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Phosphate Ion at 2.49A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / Cytoplasm / Glycosyltransferase
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / URACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsTimofeev, V.I. / Pavlyuk, B.P. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
CitationJournal: To be published
Title: Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Phosphate Ion at 2.49A Resolution
Authors: Timofeev, V.I. / Pavlyuk, B.P. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
History
DepositionOct 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
F: Uridine phosphorylase
E: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,35817
Polymers162,2276
Non-polymers1,13011
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23970 Å2
ΔGint-141.5 kcal/mol
Surface area46070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.000, 124.260, 133.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uridine phosphorylase / UrdPase / UPase


Mass: 27037.896 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: udp / Plasmid: PBLUESCRIPT IISK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, DE3 / References: UniProt: P0A1F6, uridine phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 25, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.49→26.84 Å / Num. obs: 47321

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEC

2oec


Resolution: 2.51→15.98 Å
RfactorNum. reflection
Rfree0.25652 -
Rwork0.22066 -
obs-46173
Refinement stepCycle: LAST / Resolution: 2.51→15.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11225 0 70 218 11513

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