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- PDB-3f0t: Crystal structure of thymidine kinase from Herpes simplex virus t... -

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Basic information

Entry
Database: PDB / ID: 3f0t
TitleCrystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT
ComponentsThymidine kinase
KeywordsTRANSFERASE / thymidine kinase / DNA-synthesis / PET tracer / ATP-binding / DNA synthesis / Early protein / Nucleotide-binding
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-Methyl-6-(1,3-dihydroxy-isobutyl)thymine / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHerpes simplex virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPernot, L. / Perozzo, R. / Westermaier, Y. / Martic, M. / Ametamey, S. / Scapozza, L.
Citation
Journal: Nucleosides Nucleotides Nucleic Acids / Year: 2011
Title: Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.
Authors: Martic, M. / Pernot, L. / Westermaier, Y. / Perozzo, R. / Kraljevic, T.G. / Kristafor, S. / Raic-Malic, S. / Scapozza, L. / Ametamey, S.
#1: Journal: Proteins / Year: 2000
Title: Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography.
Authors: Vogt, J. / Perozzo, R. / Pautsch, A. / Prota, A. / Schelling, P. / Pilger, B. / Folkers, G. / Scapozza, L. / Schulz, G.E.
#2: Journal: Febs Lett. / Year: 1995
Title: The three-dimensional structure of thymidine kinase from herpes simplex virus type 1.
Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E.
#3: 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.
History
DepositionOct 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Oct 2, 2013Group: Structure summary
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

Deposited unit
A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84910
Polymers71,8172
Non-polymers1,0338
Water5,459303
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-34.2 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 117.365, 107.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thymidine kinase


Mass: 35908.266 Da / Num. of mol.: 2 / Fragment: Residues 45-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17)
Strain: 17 / Gene: TK, UL23 / Production host: Escherichia coli (E. coli)
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NCV / N-Methyl-6-(1,3-dihydroxy-isobutyl)thymine / 6-[3-hydroxy-2-(hydroxymethyl)propyl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione / N-methyl-DHBT


Mass: 228.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→31 Å / Num. all: 48655 / Num. obs: 48655 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.111 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.4 / Num. unique all: 7028 / Rsym value: 0.385 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E2P

1e2p


Resolution: 2→31 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2438 -random
Rwork0.195 ---
obs0.211 48627 100 %-
Displacement parametersBiso mean: 31.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 62 303 5118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 397 -
Rwork0.228 --
obs-7609 100 %

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