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- PDB-3rdp: Crystal structure of thymidine kinase from herpes simplex virus t... -

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Basic information

Entry
Database: PDB / ID: 3rdp
TitleCrystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT
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 / 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
Chem-NMF / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Structure summary
Revision 1.2Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,3077
Polymers71,5582
Non-polymers7495
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-34 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.187, 118.283, 108.871
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: 35779.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: strain 17 / Gene: TK, UL23 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NMF / 6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]-1,5-dimethyl-pyrimidine-2,4-dione


Mass: 230.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15FN2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
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: X06DA / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→35.267 Å / Num. obs: 16788 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.218 / Rsym value: 0.186 / Net I/σ(I): 5.94
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2475 / Rsym value: 0.566 / % possible all: 93

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0T

3f0t


Resolution: 2.8→35.26 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 819 4.88 %RANDOM
Rwork0.2001 ---
obs0.2022 16788 90.7 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.94 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 36.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.2827 Å20 Å2-0 Å2
2--18.494 Å20 Å2
3----15.2113 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 47 81 4957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025020
X-RAY DIFFRACTIONf_angle_d0.5496853
X-RAY DIFFRACTIONf_dihedral_angle_d11.1881842
X-RAY DIFFRACTIONf_chiral_restr0.039791
X-RAY DIFFRACTIONf_plane_restr0.002875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97540.32391380.2688267493
2.9754-3.2050.29761390.2367267292
3.205-3.52720.23611190.2035266391
3.5272-4.0370.22561290.1868266391
4.037-5.08370.22131390.1566264190
5.0837-35.26260.22851550.2051265687

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