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- PDB-1ki8: CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS T... -

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Basic information

Entry
Database: PDB / ID: 1ki8
TitleCRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOVINYLDEOXYURIDINE
ComponentsTHYMIDINE KINASE
KeywordsPHOSPHOTRANSFERASE / THYMIDINE KINASE / VIRIDAE / DS-DNA ENVELOPED VIRUSES / HERPESVIRIDAE / ALPHAHERPESVIRINAE / SUBSTRATE ANALOG / 5-BROMOVINYLDEOXYURIDINE
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-BROMOVINYLDEOXYURIDINE / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHerpes simplex virus
MethodX-RAY DIFFRACTION / MIR, NCS IMPROVEMENT, SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KIN / Resolution: 2.2 Å
AuthorsChampness, J.N. / Bennett, M.S. / Wien, F. / Visse, R. / Summers, W.C. / Sanderson, M.R.
Citation
Journal: Proteins / Year: 1998
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: Journal: Yale J.Biol.Med. / Year: 1996
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: Journal: Nat.Struct.Biol. / Year: 1995
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: Journal: J.Gen.Virol. / Year: 1988
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: Journal: J.Mol.Biol. / Year: 1988
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: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
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
DepositionMay 15, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4176
Polymers71,5582
Non-polymers8584
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-63 kcal/mol
Surface area21940 Å2
MethodPISA
2
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,83312
Polymers143,1164
Non-polymers1,7178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11990 Å2
ΔGint-135 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.400, 116.900, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92877, 0.32272, 0.18233), (0.31708, 0.43701, 0.84171), (0.19196, 0.83957, -0.50821)
Vector: 27.21921, -1.62489, -7.39048)

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Components

#1: Protein THYMIDINE KINASE / / TK


Mass: 35779.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17)
Genus: Simplexvirus / Species: Human herpesvirus 1Herpesviridae / Strain: 17 / Gene: TK / Plasmid: PT7\:HSVTK / Gene (production host): TK / Production host: Escherichia coli (E. coli) / Strain (production host): SY211
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BVD / 5-BROMOVINYLDEOXYURIDINE / Brivudine


Mass: 333.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13BrN2O5 / Comment: antivirus*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 54 %
Crystal growMethod: 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 drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 mg/mlprotein1drop
240 mMTris-Cl1drop
33 mMdithiothreitol1drop
40.2 mMdeoxythymidine1drop
530 %satammonium sulfate1reservoir
6200 mMTris-Cl1reservoir
73 mMdithiothreitol1reservoir
80.2 mMdeoxythymidine1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: OTWINOWSKI MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest 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 shellResolution: 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

Software
NameVersionClassification
SOLOMONphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR, NCS IMPROVEMENT, SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KIN
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.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2853 10 %RANDOM
Rwork0.199 ---
obs0.199 28510 78 %-
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 48 249 4973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.921
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.74
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.724
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53
X-RAY DIFFRACTIONx_mcangle_it24
X-RAY DIFFRACTIONx_scbond_it1.53
X-RAY DIFFRACTIONx_scangle_it24
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 207 -
Rwork0.287 1917 -
obs--78.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION11KIN_PARHCSDX.PRO1KIN_SO4.TOP
X-RAY DIFFRACTION21KIN_PARAM19.SOL1KIN_TOPH19.SOL
X-RAY DIFFRACTION31KIN_PARNAH1E.DNA1KIN_TOPHCSDX.PRO
X-RAY DIFFRACTION41KIN_SO4.PARBVDU.TOP
X-RAY DIFFRACTION5BVDU.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.74
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.724

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