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- PDB-3nbq: Human uridine phosphorylase 1 (hUPP1) with 5-fluorouracil -

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Basic information

Entry
Database: PDB / ID: 3nbq
TitleHuman uridine phosphorylase 1 (hUPP1) with 5-fluorouracil
ComponentsUridine phosphorylase 1
KeywordsTRANSFERASE / nucleoside phosphorylase / 5-fluorouracil / chemotherapy
Function / homology
Function and homology information


deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / UMP catabolic process / dUMP catabolic process / uridine catabolic process / Pyrimidine catabolism / Pyrimidine salvage ...deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / UMP catabolic process / dUMP catabolic process / uridine catabolic process / Pyrimidine catabolism / Pyrimidine salvage / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleobase-containing compound metabolic process / cellular response to glucose starvation / nucleoplasm / 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
5-FLUOROURACIL / Uridine phosphorylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRoosild, T.P.
CitationJournal: Plos One / Year: 2010
Title: Active site conformational dynamics in human uridine phosphorylase 1.
Authors: Roosild, T.P. / Castronovo, S.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 1
B: Uridine phosphorylase 1
C: Uridine phosphorylase 1
D: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7238
Polymers144,2024
Non-polymers5204
Water2,306128
1
A: Uridine phosphorylase 1
B: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3614
Polymers72,1012
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-25 kcal/mol
Surface area22040 Å2
MethodPISA
2
C: Uridine phosphorylase 1
D: Uridine phosphorylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3614
Polymers72,1012
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-22 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.317, 85.281, 260.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 78 - 84 / Label seq-ID: 96 - 102

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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


Mass: 36050.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UP, UPP1 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16831, uridine phosphorylase
#2: Chemical
ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 3350, 100mM Bis-Tris buffer pH 5.5, 160mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Feb 18, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58528 / % possible obs: 94.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Χ2: 0.987 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.10.24741400.95767.4
2.38-2.482.50.22249310.93281.1
2.48-2.592.90.20357250.97193
2.59-2.733.90.17260981.06999.9
2.73-2.94.10.13261790.965100
2.9-3.124.10.09461750.95100
3.12-3.444.10.06962120.941100
3.44-3.934.10.05262130.99299.9
3.93-4.9540.0462961.02199.9
4.95-503.80.03365591.0299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.66 Å33.81 Å
Translation2.66 Å33.81 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.779 / SU B: 8.283 / SU ML: 0.202 / SU R Cruickshank DPI: 0.369 / SU Rfree: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2897 5 %RANDOM
Rwork0.222 ---
obs0.225 58444 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.58 Å2 / Biso mean: 37.233 Å2 / Biso min: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--2.07 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9012 0 36 128 9176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229196
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.98512420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91951168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29723.656372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.634151640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681564
X-RAY DIFFRACTIONr_chiral_restr0.0860.21432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026792
X-RAY DIFFRACTIONr_nbd_refined0.1950.24128
X-RAY DIFFRACTIONr_nbtor_refined0.2990.26292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.24
X-RAY DIFFRACTIONr_mcbond_it0.7191.56005
X-RAY DIFFRACTIONr_mcangle_it1.21629364
X-RAY DIFFRACTIONr_scbond_it1.69333610
X-RAY DIFFRACTIONr_scangle_it2.6424.53056
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
28TIGHT POSITIONAL0.050.05
28TIGHT POSITIONAL0.060.05
28TIGHT POSITIONAL0.030.05
28TIGHT POSITIONAL0.030.05
24LOOSE POSITIONAL1.685
24LOOSE POSITIONAL1.165
24LOOSE POSITIONAL0.95
24LOOSE POSITIONAL1.395
28TIGHT THERMAL0.150.5
28TIGHT THERMAL0.070.5
28TIGHT THERMAL0.130.5
28TIGHT THERMAL0.060.5
24LOOSE THERMAL1.0410
24LOOSE THERMAL0.8310
24LOOSE THERMAL1.0810
24LOOSE THERMAL0.5510
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 155 -
Rwork0.265 2789 -
all-2944 -
obs--65.2 %

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