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- PDB-3kvv: Trapping of an oxocarbenium ion intermediate in UP crystals -

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Basic information

Entry
Database: PDB / ID: 3kvv
TitleTrapping of an oxocarbenium ion intermediate in UP crystals
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Oxocarbenium Ion / Glycal / Pyrimidine Salvage / Uridine Phosphorylase / Cytoplasm / Glycosyltransferase
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / 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
1,4-anhydro-D-erythro-pent-1-enitol / 5-FLUOROURACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPaul, D. / O'Leary, S. / Rajashankar, K. / Bu, W. / Toms, A. / Settembre, E. / Sanders, J. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: Glycal formation in crystals of uridine phosphorylase.
Authors: Paul, D. / O'Leary, S.E. / Rajashankar, K. / Bu, W. / Toms, A. / Settembre, E.C. / Sanders, J.M. / Begley, T.P. / Ealick, S.E.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Apr 22, 2020Group: Atomic model / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jul 29, 2020Group: Derived calculations / Category: struct_site / struct_site_gen / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,28424
Polymers163,1346
Non-polymers2,15018
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21440 Å2
ΔGint-229 kcal/mol
Surface area42750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.864, 92.864, 145.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Uridine phosphorylase / / UrdPase / UPase


Mass: 27189.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: UDP / Plasmid: XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12758, uridine phosphorylase
#2: Chemical
ChemComp-URF / 5-FLUOROURACIL / Fluorouracil


Mass: 130.077 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-R2B / 1,4-anhydro-D-erythro-pent-1-enitol


Type: D-saccharide / Mass: 132.115 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C5H8O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 295 K / pH: 6.3
Details: 5% PEG4K, 5% glycerol, 100 mM MES, pH 6.3, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 123229
Reflection shellHighest resolution: 1.8 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.52 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 0.03 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 5992 4.97 %
Rwork0.173 --
obs0.175 120598 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.26 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.767 Å2-1.215 Å20 Å2
2---0.767 Å20 Å2
3---1.533 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10861 0 138 698 11697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711173
X-RAY DIFFRACTIONf_angle_d1.17415177
X-RAY DIFFRACTIONf_dihedral_angle_d16.9163959
X-RAY DIFFRACTIONf_chiral_restr0.0721807
X-RAY DIFFRACTIONf_plane_restr0.0051945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8031-1.82360.25321110.24552299X-RAY DIFFRACTION55
1.8236-1.8450.27061460.22862748X-RAY DIFFRACTION68
1.845-1.86750.26041720.22513101X-RAY DIFFRACTION76
1.8675-1.89110.27281920.21293432X-RAY DIFFRACTION84
1.8911-1.9160.25771840.20023759X-RAY DIFFRACTION92
1.916-1.94220.24461870.19113825X-RAY DIFFRACTION94
1.9422-1.970.20111830.17933986X-RAY DIFFRACTION96
1.97-1.99940.22172260.18523884X-RAY DIFFRACTION96
1.9994-2.03060.24772140.18363951X-RAY DIFFRACTION97
2.0306-2.06390.2291760.17584081X-RAY DIFFRACTION97
2.0639-2.09940.22152040.17764001X-RAY DIFFRACTION98
2.0994-2.13760.22452060.17883935X-RAY DIFFRACTION98
2.1376-2.17870.21042320.17343993X-RAY DIFFRACTION98
2.1787-2.22310.2221940.1683996X-RAY DIFFRACTION98
2.2231-2.27140.23562060.17794039X-RAY DIFFRACTION98
2.2714-2.32420.20371950.16844087X-RAY DIFFRACTION99
2.3242-2.38230.18951940.16974013X-RAY DIFFRACTION98
2.3823-2.44660.20772250.16983965X-RAY DIFFRACTION98
2.4466-2.51850.19372530.16173998X-RAY DIFFRACTION98
2.5185-2.59970.21132070.16993958X-RAY DIFFRACTION98
2.5997-2.69250.23352340.18244000X-RAY DIFFRACTION98
2.6925-2.80020.21932150.1723988X-RAY DIFFRACTION98
2.8002-2.92740.20422000.17434014X-RAY DIFFRACTION98
2.9274-3.08140.18412040.17233986X-RAY DIFFRACTION97
3.0814-3.2740.21051970.16943994X-RAY DIFFRACTION97
3.274-3.5260.19462150.1593931X-RAY DIFFRACTION97
3.526-3.87940.16672090.15663952X-RAY DIFFRACTION97
3.8794-4.43750.19242120.15093926X-RAY DIFFRACTION96
4.4375-5.57850.17352050.16453923X-RAY DIFFRACTION96
5.5785-23.52490.17981940.17743841X-RAY DIFFRACTION94
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION35f_b1.par
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5R1G_new.param

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