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- PDB-4oqm: 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: 4oqm | ||||||
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Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-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 / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L. | ||||||
![]() | ![]() Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 105.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 |
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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 | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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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: 2.2→39.1 Å / Num. all: 35059 / Num. obs: 35059 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.089 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4861 / Rsym value: 0.452 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3F0T Resolution: 2.2→39.091 Å / SU ML: 0.21 / Isotropic thermal model: 30.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.49 / 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: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.091 Å
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Refine LS restraints |
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LS refinement shell |
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