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- PDB-2y8c: Plasmodium falciparum dUTPase in complex with a trityl ligand -

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Basic information

Entry
Database: PDB / ID: 2y8c
TitlePlasmodium falciparum dUTPase in complex with a trityl ligand
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
KeywordsHYDROLASE / MALARIA
Function / homology
Function and homology information


tRNA metabolic process / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / DNA replication / magnesium ion binding / identical protein binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DUQ / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaragana, B. / McCarthy, O. / Sanchez, P. / Bosch, C. / Kaiser, M. / Brun, R. / Whittingham, J.L. / Roberts, S. / Zhou, X.-X. / Wilson, K.S. ...Baragana, B. / McCarthy, O. / Sanchez, P. / Bosch, C. / Kaiser, M. / Brun, R. / Whittingham, J.L. / Roberts, S. / Zhou, X.-X. / Wilson, K.S. / Johansson, N.G. / Gonzalez-Pacanowska, D. / Gilbert, I.H.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Beta-Branched Acyclic Nucleoside Analogues as Inhibitors of Plasmodium Falciparum Dutpase
Authors: Baragana, B. / Mccarthy, O. / Sanchez, P. / Bosch, C. / Kaiser, M. / Brun, R. / Whittingham, J.L. / Roberts, S. / Zhou, X.-X. / Wilson, K.S. / Johansson, N.G. / Gonzalez-Pacanowska, D. / Gilbert, I.H.
History
DepositionFeb 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _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: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
B: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
C: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5428
Polymers58,8103
Non-polymers1,7335
Water2,180121
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-53.2 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 77.160, 110.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE-HYDROLASE


Mass: 19603.174 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: ONE TRITYL ANALOGUE ASSOCIATED WITH EACH PROTEIN CHAIN
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8II92, dUTP diphosphatase
#2: Chemical ChemComp-DUQ / (2S)-2-[(2,4-dioxopyrimidin-1-yl)methyl]-N-(2-hydroxyethyl)-4-trityloxy-butanamide / 5'-TRITYLATED DEOXYURIDINE ANALOGUE


Mass: 513.584 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H31N3O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6 / Details: 3.3M AMMONIUM SULPHATE, 0.1M BIS-TRIS PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→38.9 Å / Num. obs: 35984 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYQ

1vyq


Resolution: 2.1→38.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.801 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24048 1902 5 %RANDOM
Rwork0.18793 ---
obs0.1905 35984 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 124 121 3399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2582.0254271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9165387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81424.538119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11815523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.021513
X-RAY DIFFRACTIONr_chiral_restr0.2220.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 127 -
Rwork0.261 2620 -
obs--100 %

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