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- PDB-4u2k: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

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Basic information

Entry
Database: PDB / ID: 4u2k
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / metal ion binding / cytosol
Similarity search - Function
Uridine phosphorylase / 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-4WR / Chem-M5F / DI(HYDROXYETHYL)ETHER / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To Be Published
Title: X-ray structure uridine phosphorylase from Vibrio cholerae in complex with new anticancer compound at 1.17 A resolution
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,31021
Polymers162,6546
Non-polymers1,65615
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22680 Å2
ΔGint-81 kcal/mol
Surface area45280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.280, 91.280, 137.227
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase


Mass: 27108.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: udp, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 7 types, 607 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-4WR / 1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione


Mass: 202.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11FN4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-M5F / 1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione


Mass: 202.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11FN4O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.000039 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000039 Å / Relative weight: 1
ReflectionResolution: 2.13→38.003 Å / Num. all: 71570 / Num. obs: 71570 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 20.22 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.115 / Rsym value: 0.109 / Net I/av σ(I): 4.61 / Net I/σ(I): 13.8 / Num. measured all: 708536
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.13-2.259.40.4291.898132104380.1460.4295.2100
2.25-2.389.40.3182.49270499020.1090.3186.599.9
2.38-2.559.80.2323.39106593060.0780.2328.5100
2.55-2.7510.20.1814.18881186790.060.18110.4100
2.75-3.01100.1315.37923379130.0440.13113.6100
3.01-3.3710.50.0986.37594372490.0320.09818.3100
3.37-3.8910.10.086.56385662980.0260.0823.2100
3.89-4.7610.30.0727.15548853890.0240.07227.1100
4.76-6.749.90.0767.14111741360.0250.07625.1100
6.74-38.0039.80.0667.12218722600.0220.06629.199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation38 Å2.04 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
SCALA3.3.20data scaling
MOLREP11.0.02phasing
PDB_EXTRACT3.14data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G8J

4g8j


Resolution: 2.13→19.771 Å / FOM work R set: 0.7661 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 2155 3.02 %
Rwork0.2085 69100 -
obs0.2101 71255 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.44 Å2 / Biso mean: 23.23 Å2 / Biso min: 4.26 Å2
Refinement stepCycle: final / Resolution: 2.13→19.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11063 0 111 630 11804
Biso mean--29.41 22.06 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911565
X-RAY DIFFRACTIONf_angle_d1.21915686
X-RAY DIFFRACTIONf_chiral_restr0.0761839
X-RAY DIFFRACTIONf_plane_restr0.0052027
X-RAY DIFFRACTIONf_dihedral_angle_d15.0444272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.17950.29141490.21614613476299
2.1795-2.23390.3011410.212345634704100
2.2339-2.29430.28831500.2064627477799
2.2943-2.36170.30881570.20584552470999
2.3617-2.43780.30431210.205246454766100
2.4378-2.52470.28911350.198446004735100
2.5247-2.62560.29421560.203146164772100
2.6256-2.74480.27281390.210646104749100
2.7448-2.88910.2751210.209146124733100
2.8891-3.06950.27311470.221145864733100
3.0695-3.30550.30491510.214146364787100
3.3055-3.63620.24811650.20445914756100
3.6362-4.15820.23311460.199146304776100
4.1582-5.22280.20141300.195945934723100
5.2228-19.77180.241470.228746264773100

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