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- PDB-1k3f: Uridine Phosphorylase from E. coli, Refined in the Monoclinic Cry... -

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Basic information

Entry
Database: PDB / ID: 1k3f
TitleUridine Phosphorylase from E. coli, Refined in the Monoclinic Crystal Lattice
Componentsuridine phosphorylase
KeywordsTRANSFERASE / nucleoside phosphorylase / hexamer
Function / homology
Function and homology information


UMP catabolic process / uridine catabolic process / deoxyuridine phosphorylase activity / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding ...UMP catabolic process / uridine catabolic process / deoxyuridine phosphorylase activity / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMorgunova, E.Yu. / Mikhailov, A.M. / Popov, A.N. / Blagova, E.V. / Smirnova, E.A. / Vainshtein, B.K. / Mao, C. / Armstrong, S.R. / Ealick, S.E. / Komissarov, A.A. ...Morgunova, E.Yu. / Mikhailov, A.M. / Popov, A.N. / Blagova, E.V. / Smirnova, E.A. / Vainshtein, B.K. / Mao, C. / Armstrong, S.R. / Ealick, S.E. / Komissarov, A.A. / Linkova, E.V. / Burlakova, A.A. / Mironov, A.S. / Debabov, V.G.
CitationJournal: FEBS Lett. / Year: 1995
Title: Atomic structure at 2.5 A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice.
Authors: Morgunova, E.Yu. / Mikhailov, A.M. / Popov, A.N. / Blagova, E.V. / Smirnova, E.A. / Vainshtein, B.K. / Mao, C. / Armstrong, S.R. / Ealick, S.E. / Komissarov, A.A. / Linkova, E.V. / ...Authors: Morgunova, E.Yu. / Mikhailov, A.M. / Popov, A.N. / Blagova, E.V. / Smirnova, E.A. / Vainshtein, B.K. / Mao, C. / Armstrong, S.R. / Ealick, S.E. / Komissarov, A.A. / Linkova, E.V. / Burlakova, A.A. / Mironov, A.S. / Debabov, V.G.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uridine phosphorylase
B: uridine phosphorylase
C: uridine phosphorylase
D: uridine phosphorylase
E: uridine phosphorylase
F: uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)163,1346
Polymers163,1346
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18380 Å2
ΔGint-147 kcal/mol
Surface area54200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.6, 98.8, 93.7
Angle α, β, γ (deg.)90, 120.2, 90
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a hexamer of identical subunits; asymmetric unit contains a Upase hexamer. Entire hexamer is deposited,

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Components

#1: Protein
uridine phosphorylase / Upase / UDRPase


Mass: 27189.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUD7 / Production host: Escherichia coli (E. coli) / Strain (production host): AM1906 / References: UniProt: P12758, uridine phosphorylase

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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: 2.24 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: drops-0.05 M Tris-HCl and 4-6% PEG 4000; equilibrium solution-0.1M Tris-mal/NaOH pH5.91-5.96, 20-25% Peg 4000 and 0.04% sodium azide, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 MTris-HCl1drop
210-12 mg/mlprotein1drop
34-6 %PEG40001drop
40.1 MTris-mal/NaOH1reservoir
520-25 %PEG40001reservoir
60.04 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: KARD-6 / Detector: DIFFRACTOMETER / Date: Jan 5, 1994
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 50479 / Num. obs: 42403 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.097
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 84 % / Num. measured all: 116050

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: trigonal form of Upase

Resolution: 2.5→6 Å / Isotropic thermal model: isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rwork0.186 --
all0.186 50479 -
obs-42401 -
Rfree--random
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 0 0 11286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_d2.095
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.012

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