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- PDB-1osn: Crystal structure of Varicella zoster virus thymidine kinase in c... -

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Basic information

Entry
Database: PDB / ID: 1osn
TitleCrystal structure of Varicella zoster virus thymidine kinase in complex with BVDU-MP and ADP
ComponentsThymidine kinase
KeywordsTRANSFERASE / human herpes virus 3 / chickenpox / thymidine kinase / BVDU-MP
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-BVP / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 3 (Varicella-zoster virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBird, L.E. / Ren, J. / Wright, A. / Leslie, K.D. / Degreve, B. / Balzarini, J. / Stammers, D.K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of varicella zoster virus thymidine kinase
Authors: Bird, L.E. / Ren, J. / Wright, A. / Leslie, K.D. / Degreve, B. / Balzarini, J. / Stammers, D.K.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,88512
Polymers151,5234
Non-polymers3,3618
Water362
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4426
Polymers75,7622
Non-polymers1,6814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-53 kcal/mol
Surface area26090 Å2
MethodPISA
2
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4426
Polymers75,7622
Non-polymers1,6814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-49 kcal/mol
Surface area25080 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-113 kcal/mol
Surface area48680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.700, 54.200, 167.800
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere are two biological dimers in the asymmetric unit

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Components

#1: Protein
Thymidine kinase / VZV-TK


Mass: 37880.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 (Varicella-zoster virus)
Genus: Varicellovirus / Plasmid: pGEX6p1VZV-TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0C0E6, thymidine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-BVP / (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / BVDU-MP


Type: DNA linking / Mass: 413.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14BrN2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.21 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 20000, sodium acetate, ATP, BVDU, MgCl2, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
20.4 mMATP1drop
30.2 mMBVDU1drop
40.6 mM1dropMgCl2
5100 mMsodium acetate1reservoirpH4.5 or 5.0
66-11 %(w/v)PEG200001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 167134 / % possible obs: 99.9 % / Observed criterion σ(I): -0.5 / Redundancy: 5.6 % / Biso Wilson estimate: 77.2 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 4.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2925 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Num. obs: 30040 / Num. measured all: 167134
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 2925

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HSV-1 TK (1e2k)

1e2k


Resolution: 3.2→29.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1354083.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1490 5 %RANDOM
Rwork0.235 ---
obs-30027 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.1894 Å2 / ksol: 0.270284 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-30.72 Å20 Å2-8.94 Å2
2---15.18 Å20 Å2
3----15.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9855 0 181 2 10038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.93
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 143 4.9 %
Rwork0.359 2760 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0086
X-RAY DIFFRACTIONc_angle_deg1.32

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