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- PDB-4oqn: Crystal structure of thymidine kinase from herpes simplex virus t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oqn | ||||||
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Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with EdU | ||||||
![]() | Thymidine kinase | ||||||
![]() | TRANSFERASE / DNA SYNTHESIS / THYMIDINE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / 5-ETHYNYLURIDINE NUCLEOSIDE DERIVATIVE | ||||||
Function / homology | ![]() TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N.W. / Scapozza, L. | ||||||
![]() | ![]() Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with EdU Authors: Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N.W. / 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 103.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f0tS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: 17 / Gene: TK, TK (UL23), UL23 / Plasmid: pGEX-6P-2 / Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.6 Å / Num. all: 32116 / Num. obs: 32116 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.092 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4592 / Rsym value: 0.343 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3F0T Resolution: 2.3→39.598 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.99 / 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: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.598 Å
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Refine LS restraints |
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LS refinement shell |
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