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Yorodumi- PDB-4ivr: Crystal structure of thymidine kinase from herpes simplex virus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ivr | ||||||
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Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10 | ||||||
Components | Thymidine kinase | ||||||
Keywords | TRANSFERASE / DNA synthesis / PET imaging TRACER / ATP binding / 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: 2.4 Å | ||||||
Authors | Pernot, L. / Novakovic, I. / Westermaier, Y. / Perozzo, R. / Raic-Malic, S. / Scapozza, L. | ||||||
Citation | Journal: To be Published Title: New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer Authors: Pernot, L. / Novakovic, I. / Perozzo, R. / Raic-Malic, S. / Scapozza, L. #1: 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. #2: Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: A new N-methyl thymine derivative comprising a dihydroxyisobutenyl unit as ligand for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK). Authors: Kristafor, S. / Novakovic, I. / Gazivoda Kraljevic, T. / Kraljevic Pavelic, S. / Lucin, P. / Westermaier, Y. / Pernot, L. / Scapozza, L. / Ametamey, S.M. / Raic-Malic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ivr.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ivr.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ivr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ivr_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 4ivr_full_validation.pdf.gz | 476.4 KB | Display | |
Data in XML | 4ivr_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4ivr_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/4ivr ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4ivr | HTTPS FTP |
-Related structure data
Related structure data | 4ivpC 4ivqC 4jbxC 4jbyC 3f0tS 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 on special symmetry positions |
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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: 17 / Gene: TK, TK (UL23), UL23 / Plasmid: pGEX-6P-2 / 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: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.9-1.2 M lithium sulfate, 1 mM DTT, 0.1 M HEPES, pH 7.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 11, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40.33 Å / Num. obs: 27904 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.124 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4019 / Rsym value: 0.33 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F0T Resolution: 2.4→40.33 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→40.33 Å
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Refine LS restraints |
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LS refinement shell |
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