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- PDB-3ku4: Trapping of an oxocarbenium ion intermediate in UP crystals -

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Basic information

Entry
Database: PDB / ID: 3ku4
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
Uridine phosphorylase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0768
Polymers135,6924
Non-polymers3844
Water17,186954
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0384
Polymers67,8462
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-59 kcal/mol
Surface area21870 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0384
Polymers67,8462
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-65 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.108, 74.108, 266.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Uridine phosphorylase /


Mass: 33922.980 Da / Num. of mol.: 4
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / 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 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. all: 83503 / Num. obs: 78314 / Biso Wilson estimate: 22.89 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→50 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.854 / SU ML: 0.48 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 3902 4.98 %
Rwork0.179 --
obs0.181 78293 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.5 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 110.87 Å2 / Biso mean: 25.845 Å2 / Biso min: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.118 Å20 Å2-0 Å2
2--3.118 Å20 Å2
3----6.237 Å2
Refinement stepCycle: LAST / Resolution: 2.099→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8845 0 20 954 9819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089044
X-RAY DIFFRACTIONf_angle_d1.14112230
X-RAY DIFFRACTIONf_chiral_restr0.0821380
X-RAY DIFFRACTIONf_plane_restr0.0051592
X-RAY DIFFRACTIONf_dihedral_angle_d17.2153282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.099-2.1250.2291080.1962654276292
2.125-2.1520.2551600.1922749290998
2.152-2.180.2531220.1892706282894
2.18-2.210.2711330.192735286898
2.21-2.2420.2331430.1842706284995
2.242-2.2750.2321400.1862757289798
2.275-2.3110.2461380.1792687282595
2.311-2.3490.2541690.1862712288197
2.349-2.3890.2551470.1792754290195
2.389-2.4320.2521480.1842721286998
2.432-2.4790.2561520.1782657280994
2.479-2.530.2461560.1992688284497
2.53-2.5850.2271530.1862687284095
2.585-2.6450.2421550.1812701285694
2.645-2.7110.2371140.1872721283596
2.711-2.7840.2491300.1872684281495
2.784-2.8660.2731400.1912682282294
2.866-2.9590.2471270.1912691281894
2.959-3.0640.2371460.1912656280294
3.064-3.1870.2141280.182654278294
3.187-3.3320.2281310.1722599273093
3.332-3.5070.2051370.1772636277392
3.507-3.7270.2071470.1662592273992
3.727-4.0140.1851650.1572562272792
4.014-4.4170.1791530.1482516266989
4.417-5.0540.1731390.1452540267990
5.054-6.3610.2161120.1952508262087
6.361-33.1460.2171090.1822436254584

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