[English] 日本語
Yorodumi- PDB-3t64: 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t64 | ||||||
---|---|---|---|---|---|---|---|
Title | 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / dUTP binding / Nucleus / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 3D7 (eukaryote) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. ...Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H. | ||||||
Citation | Journal: Chemmedchem / Year: 2011 Title: Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase. Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / ...Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3t64.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3t64.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t64_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3t64_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3t64_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3t64_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t64 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t64 | HTTPS FTP |
-Related structure data
Related structure data | 3t60C 3t6yC 3t70C 1vyqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20632.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: PF11_0282 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8II92, dUTP diphosphatase #2: Protein/peptide | | Mass: 298.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.45 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→36.2 Å / Num. all: 74358 / Num. obs: 74358 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.65→36.2 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VYQ Resolution: 1.65→34.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.699 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.562 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→34.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
|