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Open data
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Basic information
Entry | Database: PDB / ID: 1p6x | ||||||
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Title | Crystal structure of EHV4-TK complexed with Thy and SO4 | ||||||
![]() | Thymidine kinase | ||||||
![]() | TRANSFERASE / P-loop / Lid | ||||||
Function / homology | ![]() TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
![]() | ![]() Title: Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases. Authors: Gardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.2 KB | Display | ![]() |
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PDB format | ![]() | 118.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.5 KB | Display | ![]() |
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Full document | ![]() | 478.8 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p72SC ![]() 1p73C ![]() 1p75C ![]() 1p7cC S: Starting model for refinement C: citing same article ( |
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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: 37013.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Varicellovirus / Strain: 1942 / Gene: TK / Plasmid: pUT699 / Production host: ![]() ![]() #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: 2.72 Å3/Da / Density % sol: 54.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, MES, Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 54599 |
Reflection | *PLUS Num. all: 423469 / % possible obs: 99.6 % / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P72 Resolution: 2→24.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.105 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.332 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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