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- PDB-3p0e: Structure of hUPP2 in an active conformation with bound 5-benzyla... -

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Basic information

Entry
Database: PDB / ID: 3p0e
TitleStructure of hUPP2 in an active conformation with bound 5-benzylacyclouridine
ComponentsUridine phosphorylase 2
KeywordsTRANSFERASE / uridine phosphorylase
Function / homology
Function and homology information


uridine metabolic process / type III intermediate filament / deoxyuridine phosphorylase activity / CMP catabolic process / dCMP catabolic process / UMP catabolic process / uridine catabolic process / Pyrimidine salvage / Pyrimidine catabolism / uridine phosphorylase ...uridine metabolic process / type III intermediate filament / deoxyuridine phosphorylase activity / CMP catabolic process / dCMP catabolic process / UMP catabolic process / uridine catabolic process / Pyrimidine salvage / Pyrimidine catabolism / uridine phosphorylase / nucleoside metabolic process / uridine phosphorylase activity / UMP salvage / identical protein binding / cytosol
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
Chem-BAU / PHOSPHATE ION / Uridine phosphorylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRoosild, T.P. / Castronovo, S. / Villoso, A.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity.
Authors: Roosild, T.P. / Castronovo, S. / Villoso, A. / Ziemba, A. / Pizzorno, G.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 2
B: Uridine phosphorylase 2
C: Uridine phosphorylase 2
D: Uridine phosphorylase 2
E: Uridine phosphorylase 2
F: Uridine phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,62318
Polymers199,3966
Non-polymers2,22812
Water6,467359
1
A: Uridine phosphorylase 2
B: Uridine phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2086
Polymers66,4652
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-62 kcal/mol
Surface area21350 Å2
MethodPISA
2
C: Uridine phosphorylase 2
D: Uridine phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2086
Polymers66,4652
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-61 kcal/mol
Surface area21520 Å2
MethodPISA
3
E: Uridine phosphorylase 2
F: Uridine phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2086
Polymers66,4652
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-65 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.342, 56.137, 141.389
Angle α, β, γ (deg.)90.000, 96.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uridine phosphorylase 2 / UrdPase 2 / UPase 2


Mass: 33232.609 Da / Num. of mol.: 6 / Fragment: UNP residues 21-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPP2 / Plasmid: pJexpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95045, uridine phosphorylase
#2: Chemical
ChemComp-BAU / 1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 276.288 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H16N2O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 134252 / % possible obs: 92.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.153 / Χ2: 1.056 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.071.30.478190.92154.3
2.07-2.151.50.418118370.948182
2.15-2.251.80.385137151.007195.3
2.25-2.372.30.35142951.047199
2.37-2.522.50.28143891.09199.3
2.52-2.712.60.217143741.094199.3
2.71-2.992.60.171144561.061199.3
2.99-3.422.60.137144091.047199.1
3.42-4.312.60.14144601.05198.6
4.31-502.60.134144981.064196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.24 Å35.44 Å
Translation2.24 Å35.44 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2583 / WRfactor Rwork: 0.2177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8291 / SU B: 4.321 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1904 / SU Rfree: 0.1679 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 6734 5 %RANDOM
Rwork0.205 ---
obs0.2069 134248 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.16 Å2 / Biso mean: 33.1254 Å2 / Biso min: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-1.05 Å2
2--1.72 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13496 0 150 359 14005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213964
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.98618854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89751728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10823.473596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.759152482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.361591
X-RAY DIFFRACTIONr_chiral_restr0.0950.22132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210357
X-RAY DIFFRACTIONr_nbd_refined0.2040.26151
X-RAY DIFFRACTIONr_nbtor_refined0.3080.29662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2666
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.216
X-RAY DIFFRACTIONr_mcbond_it1.3851.58876
X-RAY DIFFRACTIONr_mcangle_it1.569213858
X-RAY DIFFRACTIONr_scbond_it2.835735
X-RAY DIFFRACTIONr_scangle_it4.0344.54988
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 225 -
Rwork0.264 4803 -
all-5028 -
obs--47.51 %

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