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- PDB-1sq6: Plasmodium falciparum homolog of Uridine phosphorylase/Purine nuc... -

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Basic information

Entry
Database: PDB / ID: 1sq6
TitlePlasmodium falciparum homolog of Uridine phosphorylase/Purine nucleoside phosphorylase
Componentsuridine phosphorylase, putative
KeywordsTRANSFERASE / structural genomics / alpha+beta / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRobien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.
Authors: Schnick, C. / Robien, M.A. / Brzozowski, A.M. / Dodson, E.J. / Murshudov, G.N. / Anderson, L. / Luft, J.R. / Mehlin, C. / Hol, W.G. / Brannigan, J.A. / Wilkinson, A.J.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS ARE NOT CERTAIN THE BIOLOGICAL UNIT IS A MONOMER.
Remark 999SEQUENCE THE DEPOSITORS NOTE THAT THE ABSENCE OF ELECTRON DENSITY FOR PHE 140 MAY BE DUE TO A ...SEQUENCE THE DEPOSITORS NOTE THAT THE ABSENCE OF ELECTRON DENSITY FOR PHE 140 MAY BE DUE TO A DISORDERED SIDE CHAIN OR ALTERNATIVELY MAY BE DUE TO A UNEXPECTED CLONING ARTIFACT.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3002
Polymers28,2041
Non-polymers961
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: uridine phosphorylase, putative
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)169,79912
Polymers169,2226
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
crystal symmetry operation16_455y-2/3,x+2/3,-z+2/31
crystal symmetry operation17_675x-y+4/3,-y+8/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area20780 Å2
ΔGint-217 kcal/mol
Surface area45850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.087, 95.087, 134.786
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein uridine phosphorylase, putative /


Mass: 28203.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PlasmoDB chr5.gen_243 / Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star/DE3 / References: UniProt: Q8I3X4, uridine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, ammonium sulfate, MOPS, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2003 / Details: Double crystal Si(111) 50 micron collimator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→28.26 Å / Num. all: 8025 / Num. obs: 8025 / % possible obs: 69.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17 Å2 / Rsym value: 0.136 / Net I/σ(I): 16
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 215 / Rsym value: 0.418 / % possible all: 22

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→28.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.17 / SU ML: 0.219 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.134 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26501 354 4.7 %RANDOM
Rwork0.18021 ---
all0.18403 7135 --
obs0.18403 7135 79.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 5 48 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211737
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9762346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315223
X-RAY DIFFRACTIONr_chiral_restr0.080.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021261
X-RAY DIFFRACTIONr_nbd_refined0.1990.2793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.212
X-RAY DIFFRACTIONr_mcbond_it1.85541112
X-RAY DIFFRACTIONr_mcangle_it3.28661791
X-RAY DIFFRACTIONr_scbond_it4.1566625
X-RAY DIFFRACTIONr_scangle_it6.1068555
LS refinement shellResolution: 2.4→2.529 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.434 27
Rwork0.263 551
obs-573

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