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- PDB-4jbx: Crystal structure of thymidine kinase from Herpes simplex virus t... -

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Basic information

Entry
Database: PDB / ID: 4jbx
TitleCrystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with SK-78
ComponentsThymidine kinase
KeywordsTRANSFERASE / DNA synthesis / PET imaging TRACER / ATP binding / 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-SK7 / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPernot, L. / Novakovic, I. / Westermaier, Y. / Perozzo, R. / Raic-Malic, S. / Scapozza, L.
Citation
Journal: To be Published
Title: New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer
Authors: Pernot, L. / Novakovic, I. / Perozzo, R. / Raic-Malic, S. / Scapozza, L.
#1: 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.
#2: Journal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: A new N-methyl thymine derivative comprising a dihydroxyisobutenyl unit as ligand for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK).
Authors: Kristafor, S. / Novakovic, I. / Gazivoda Kraljevic, T. / Kraljevic Pavelic, S. / Lucin, P. / Westermaier, Y. / Pernot, L. / Scapozza, L. / Ametamey, S.M. / Raic-Malic, S.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Experimental preparation / Structure summary
Revision 1.2Sep 20, 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)72,90711
Polymers71,8172
Non-polymers1,0919
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-112 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.486, 118.314, 108.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-782-

HOH

31A-785-

HOH

41A-810-

HOH

51A-817-

HOH

61B-508-

HOH

71B-512-

HOH

81B-568-

HOH

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Components

#1: Protein Thymidine kinase / HSV1-TK


Mass: 35908.266 Da / Num. of mol.: 2 / Fragment: UNP residues 45-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: 17 / Gene: TK, TK (UL23), UL23 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SK7 / 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione


Mass: 226.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.9-1.2 M lithium sulfate, 1 mM DTT, 0.1 M 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: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 2, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→33.02 Å / Num. all: 42784 / Num. obs: 42705 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 26.53 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.085 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.7 / Num. unique all: 6149 / Rsym value: 0.419 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F0T

3f0t


Resolution: 2.1→33.017 Å / SU ML: 0.19 / Isotropic thermal model: NONE / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2000 4.69 %RANDOM
Rwork0.1737 ---
all0.1969 42784 --
obs0.1754 42672 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 66 276 5041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074893
X-RAY DIFFRACTIONf_angle_d1.0726682
X-RAY DIFFRACTIONf_dihedral_angle_d12.5271778
X-RAY DIFFRACTIONf_chiral_restr0.072774
X-RAY DIFFRACTIONf_plane_restr0.005846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.25571410.20532876X-RAY DIFFRACTION99
2.1525-2.21070.24611390.18622826X-RAY DIFFRACTION99
2.2107-2.27570.22931410.18542870X-RAY DIFFRACTION99
2.2757-2.34920.23261420.17772876X-RAY DIFFRACTION100
2.3492-2.43310.23371400.18082857X-RAY DIFFRACTION100
2.4331-2.53050.22331430.17362881X-RAY DIFFRACTION100
2.5305-2.64560.23831420.18072893X-RAY DIFFRACTION100
2.6456-2.7850.24091420.17922893X-RAY DIFFRACTION100
2.785-2.95940.23991430.18812912X-RAY DIFFRACTION100
2.9594-3.18770.22791430.18892901X-RAY DIFFRACTION100
3.1877-3.50820.22541430.16992920X-RAY DIFFRACTION100
3.5082-4.01510.15341440.1542939X-RAY DIFFRACTION100
4.0151-5.05570.16071450.14672954X-RAY DIFFRACTION100
5.0557-33.02070.22291520.18813074X-RAY DIFFRACTION100

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