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- PDB-2xrf: Crystal structure of human uridine phosphorylase 2 -

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Basic information

Entry
Database: PDB / ID: 2xrf
TitleCrystal structure of human uridine phosphorylase 2
ComponentsURIDINE PHOSPHORYLASE 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


type III intermediate filament / uridine metabolic process / deoxyuridine phosphorylase activity / dCMP catabolic process / Pyrimidine catabolism / Pyrimidine salvage / uridine phosphorylase / UMP salvage / uridine catabolic process / nucleoside metabolic process ...type III intermediate filament / uridine metabolic process / deoxyuridine phosphorylase activity / dCMP catabolic process / Pyrimidine catabolism / Pyrimidine salvage / uridine phosphorylase / UMP salvage / uridine catabolic process / nucleoside metabolic process / uridine phosphorylase activity / 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
URACIL / Uridine phosphorylase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWelin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
CitationJournal: To be Published
Title: Crystal Structure of Human Uridine Phosphorylase 2
Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. ...Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
History
DepositionSep 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Non-polymer description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URIDINE PHOSPHORYLASE 2
B: URIDINE PHOSPHORYLASE 2
C: URIDINE PHOSPHORYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,21912
Polymers102,5333
Non-polymers6859
Water7,710428
1
A: URIDINE PHOSPHORYLASE 2
hetero molecules

A: URIDINE PHOSPHORYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8128
Polymers68,3552
Non-polymers4576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7830 Å2
ΔGint-49.4 kcal/mol
Surface area21250 Å2
MethodPISA
2
B: URIDINE PHOSPHORYLASE 2
C: URIDINE PHOSPHORYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8128
Polymers68,3552
Non-polymers4576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-48.8 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.280, 95.280, 186.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2030-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4352, -0.8997, 0.03449), (0.9003, -0.4349, 0.01629), (0.00034, 0.031814, 0.9993)-49.9, -25.41, 2.724
2given(-0.4253, 0.9052, 0.03861), (-0.9048, -0.4257, 0.004021), (0.02007, -0.03322, 0.9992)3.714, -56.15, -0.5935

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Components

#1: Protein URIDINE PHOSPHORYLASE 2 / URDPASE 2 / UPASE 2


Mass: 34177.703 Da / Num. of mol.: 3 / Fragment: RESIDUES 23-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: O95045, uridine phosphorylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.4 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growpH: 8 / Details: 0.2 MGCL2, 0.1 M TRIS PH 8, 25% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2010 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→34.4 Å / Num. obs: 44181 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EUE

3eue


Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9228 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 86-89 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2230 5.05 %RANDOM
Rwork0.1677 ---
obs0.1697 44177 --
Displacement parametersBiso mean: 22.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.0567 Å20 Å20 Å2
2---2.0567 Å20 Å2
3---4.1134 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6734 0 45 428 7207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016980HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039426HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3273SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1034HARMONIC5
X-RAY DIFFRACTIONt_it6980HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion2.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion917SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8516SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2438 171 5.29 %
Rwork0.175 3061 -
all0.1785 3232 -

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