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

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Basic information

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


uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytoplasm
Similarity search - Function
Uridine phosphorylase, eukaryotic / 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
2,5-anhydro-4-deoxy-D-erythro-pent-4-enitol / 5-FLUOROURACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 2.0Apr 22, 2020Group: Atomic model / Data collection / Category: atom_site / chem_comp
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 / _chem_comp.type
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

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5308
Polymers67,8462
Non-polymers6856
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-65 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.416, 82.416, 258.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uridine phosphorylase /


Mass: 33922.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: UPP1 / Plasmid: XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: A5PJH9, uridine phosphorylase
#2: Chemical ChemComp-URF / 5-FLUOROURACIL / Fluorouracil


Mass: 130.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-R2G / 2,5-anhydro-4-deoxy-D-erythro-pent-4-enitol


Type: L-saccharide / Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 295 K / pH: 6.3
Details: 18% PEG5K MME, 140 mM MgCl2, 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: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28268 / Biso Wilson estimate: 33.9 Å2
Reflection shellHighest resolution: 2.6 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 2.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.57 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1367 5.08 %
Rwork0.167 --
obs0.169 28268 94.7 %
all-28439 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.85 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 37.74 Å2
Baniso -1Baniso -2Baniso -3
1-7.943 Å20 Å2-0 Å2
2--7.943 Å20 Å2
3----15.885 Å2
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 44 120 4653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084615
X-RAY DIFFRACTIONf_angle_d1.1736234
X-RAY DIFFRACTIONf_dihedral_angle_d16.5541674
X-RAY DIFFRACTIONf_chiral_restr0.079695
X-RAY DIFFRACTIONf_plane_restr0.005810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6930.3121150.2292237X-RAY DIFFRACTION85
2.693-2.8010.2771330.1922344X-RAY DIFFRACTION89
2.801-2.9280.2141190.1762458X-RAY DIFFRACTION92
2.928-3.0820.231450.1742442X-RAY DIFFRACTION92
3.082-3.2760.231320.1682535X-RAY DIFFRACTION96
3.276-3.5280.1781410.1552618X-RAY DIFFRACTION98
3.528-3.8830.1861460.152634X-RAY DIFFRACTION98
3.883-4.4450.1721450.1352644X-RAY DIFFRACTION98
4.445-5.5980.1721410.1412744X-RAY DIFFRACTION99
5.598-43.8130.2071500.1912898X-RAY DIFFRACTION99

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