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Yorodumi- PDB-3f0t: Crystal structure of thymidine kinase from Herpes simplex virus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0t | ||||||
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Title | Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT | ||||||
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 | Herpes simplex virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. #2: Journal: Febs Lett. / Year: 1995 Title: The three-dimensional structure of thymidine kinase from herpes simplex virus type 1. Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E. #3: Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir. Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / Sanderson, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f0t.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f0t.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 3f0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f0t_validation.pdf.gz | 473.9 KB | Display | wwPDB validaton report |
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Full document | 3f0t_full_validation.pdf.gz | 489.7 KB | Display | |
Data in XML | 3f0t_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3f0t_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0t ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0t | HTTPS FTP |
-Related structure data
Related structure data | 3rdpC 1e2pS 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: 35908.266 Da / Num. of mol.: 2 / Fragment: Residues 45-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17) Strain: 17 / Gene: TK, UL23 / Production host: Escherichia coli (E. coli) References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | ChemComp-SO4 / #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: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop 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: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→31 Å / Num. all: 48655 / Num. obs: 48655 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.111 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.4 / Num. unique all: 7028 / Rsym value: 0.385 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1E2P Resolution: 2→31 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.3 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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