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Yorodumi- PDB-4oql: Crystal structure of thymidine kinase from herpes simplex virus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oql | ||||||
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Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU | ||||||
Components | Thymidine kinase | ||||||
Keywords | TRANSFERASE / DNA SYNTHESIS / THYMIDINE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / 5-ETHYNYLURIDINE NUCLEOSIDE DERIVATIVE | ||||||
Function / homology | Function and homology information TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU Authors: Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides. Authors: Neef, A.B. / Luedtke, N.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oql.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oql.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 4oql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/4oql ftp://data.pdbj.org/pub/pdb/validation_reports/oq/4oql | HTTPS FTP |
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-Related structure data
Related structure data | 3f0tS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35908.266 Da / Num. of mol.: 2 / Fragment: UNP residues 45-376 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 | 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: 2.48 Å3/Da / Density % sol: 50.48 % |
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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 PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→27.42 Å / Num. all: 41988 / Num. obs: 41988 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.085 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6052 / Rsym value: 0.33 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F0T Resolution: 2.1→27.4 Å / SU ML: 0.22 / Isotropic thermal model: 22.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.31 / 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: 22.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→27.4 Å
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Refine LS restraints |
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LS refinement shell |
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