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- PDB-1ki8: 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: 1ki8 | ||||||
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Title | CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOVINYLDEOXYURIDINE | ||||||
![]() | THYMIDINE KINASE | ||||||
![]() | PHOSPHOTRANSFERASE / THYMIDINE KINASE / VIRIDAE / DS-DNA ENVELOPED VIRUSES / HERPESVIRIDAE / ALPHAHERPESVIRINAE / SUBSTRATE ANALOG / 5-BROMOVINYLDEOXYURIDINE | ||||||
Function / homology | ![]() TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Champness, J.N. / Bennett, M.S. / Wien, F. / Visse, R. / Summers, W.C. / Sanderson, M.R. | ||||||
![]() | ![]() Title: Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands. Authors: Champness, J.N. / Bennett, M.S. / Wien, F. / Visse, R. / Summers, W.C. / Herdewijn, P. / de Clerq, E. / Ostrowski, T. / Jarvest, R.L. / Sanderson, M.R. #1: ![]() Title: 3'-Amino Thymidine Affinity Matrix for the Purification of Herpes Simplex Virus Thymidine Kinase Authors: Tung, P.P. / Respass, J. / Summers, W.C. #2: ![]() 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. #3: ![]() Title: The Complete DNA Sequence of the Long Unique Region in the Genome of Herpes Simplex Virus Type 1 Authors: Mcgeoch, D.J. / Dalrymple, M.A. / Davison, A.J. / Dolan, A. / Frame, M.C. / Mcnab, D. / Perry, L.J. / Scott, J.E. / Taylor, P. #4: ![]() Title: Purification and Crystallization of Thymidine Kinase from Herpes Simplex Virus Type 1 Authors: Sanderson, M.R. / Freemont, P.S. / Murthy, H.M. / Krane, J.F. / Summers, W.C. / Steitz, T.A. #5: ![]() Title: Nucleotide Sequence of the Thymidine Kinase Gene of Herpes Simplex Virus Type 1 Authors: Wagner, M.J. / Sharp, J.A. / Summers, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.1 KB | Display | ![]() |
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Full document | ![]() | 1023.7 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ki2C ![]() 1ki3C ![]() 1ki4C ![]() 1ki6C ![]() 1ki7C ![]() 1kimC 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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1 |
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92877, 0.32272, 0.18233), Vector: |
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Components
#1: Protein | Mass: 35779.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: 17 / Gene: TK / Plasmid: PT7\:HSVTK / Gene (production host): TK / Production host: ![]() ![]() References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING-DROP: 8ML PROTEIN SOLUTION PLUS 4ML PRECIPITATING SOLUTION EQUILIBRATED AGAINST PRECIPITATING SOLUTION AT 25 C. PROTEIN SOLUTION: HSV-TK 1.0MG/ML; 40MM TRIS-CL PH 7.5; 3MM DTT; 0.2MM ...Details: HANGING-DROP: 8ML PROTEIN SOLUTION PLUS 4ML PRECIPITATING SOLUTION EQUILIBRATED AGAINST PRECIPITATING SOLUTION AT 25 C. PROTEIN SOLUTION: HSV-TK 1.0MG/ML; 40MM TRIS-CL PH 7.5; 3MM DTT; 0.2MM DT. PRECIPITATING SOLUTION: 30% SATURATED AMMONIUM SULPHATE; 200MM TRIS-CL PH 6.75; 3MM DTT; 0.2 MM DT. EXCHANGE OF DEOXYTHYMIDINE BOUND TO THE PROTEIN FOR 5-BROMOVINYLDEOXYURIDINE WAS MADE BY WASHING THE CRYSTALS FIVE TIMES IN A 3 ML SOLUTION (33% SATURATED AMMONIUM SULPHATE; 100MM TRIS-CL PH 6.75) CONTAINING 5-BROMOVINYLDEOXYURIDINE (BVDU)., vapor diffusion - hanging drop PH range: 6.75-7.5 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: OTWINOWSKI MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.15 Å / Num. obs: 36243 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.118 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / % possible all: 92 |
Reflection | *PLUS Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS % possible obs: 92 % |
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Processing
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Refinement | Method to determine structure: ![]() Resolution: 2.2→12 Å / Isotropic thermal model: INDIVIDUAL B-FACTOR REFT. / σ(F): 2.8 Details: NCS RESTRAINTS NOT USED IN FINAL CYCLES. IN C-TERMINAL PORTIONS OF MODELLED SEGMENTS, PEPTIDE HAS BECOME SIGNIFICANTLY NON-PLANAR.
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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