+Open data
-Basic information
Entry | Database: PDB / ID: 2y8c | ||||||
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Title | Plasmodium falciparum dUTPase in complex with a trityl ligand | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
Keywords | HYDROLASE / 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 | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Baragana, 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8c.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8c.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y8c_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2y8c_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2y8c_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2y8c_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8c ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8c | HTTPS FTP |
-Related structure data
Related structure data | 1vyqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 3.3M AMMONIUM SULPHATE, 0.1M BIS-TRIS PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.1→2.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.9 Å
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Refine LS restraints |
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