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Yorodumi- PDB-3rdp: Crystal structure of thymidine kinase from herpes simplex virus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rdp | ||||||
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Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT | ||||||
Components | Thymidine kinase | ||||||
Keywords | TRANSFERASE / THYMIDINE KINASE / DNA-SYNTHESIS / PET TRACER / ATP-BINDING / DNA SYNTHESIS / EARLY PROTEIN / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pernot, L. / Perozzo, R. / Westermaier, Y. / Martic, M. / Ametamey, S. / Scapozza, L. | ||||||
Citation | Journal: Nucleosides Nucleotides Nucleic Acids / Year: 2011 Title: Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo. Authors: Martic, M. / Pernot, L. / Westermaier, Y. / Perozzo, R. / Kraljevic, T.G. / Kristafor, S. / Raic-Malic, S. / Scapozza, L. / Ametamey, S. #1: Journal: Proteins / Year: 2000 Title: Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography. Authors: Vogt, J. / Perozzo, R. / Pautsch, A. / Prota, A. / Schelling, P. / Pilger, B. / Folkers, G. / Scapozza, L. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rdp.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdp.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rdp_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 3rdp_full_validation.pdf.gz | 477.3 KB | Display | |
Data in XML | 3rdp_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 3rdp_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdp ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdp | HTTPS FTP |
-Related structure data
Related structure data | 3f0tSC S: Starting model for refinement C: citing same article (ref.) |
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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: 35779.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Strain: strain 17 / Gene: TK, UL23 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #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: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.9-1.2M LI2SO4, 1MM DTT, 0.1M HEPES PH 7.5-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9998 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.267 Å / Num. obs: 16788 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.218 / Rsym value: 0.186 / Net I/σ(I): 5.94 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2475 / Rsym value: 0.566 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0T Resolution: 2.8→35.26 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.94 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→35.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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