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

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Basic information

Entry
Database: PDB / ID: 4ivq
TitleCrystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with IN43/5
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 / 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
Chem-I43 / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Experimental preparation / Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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)72,3277
Polymers71,5582
Non-polymers7695
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-79 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.435, 117.069, 107.775
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-693-

HOH

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Components

#1: Protein Thymidine kinase / HSV1-TK


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: 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-I43 / 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-4-methoxy-1,5-dimethylpyrimidin-2(1H)-one


Mass: 240.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging 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, HANGING 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: Feb 11, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→27.155 Å / Num. all: 56669 / Num. obs: 55929 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.054 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 6.3 / Num. unique all: 7928 / Rsym value: 0.312 / % possible all: 97.5

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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: 1.9→27.155 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1999 3.58 %RANDOM
Rwork0.1923 ---
all0.213 55831 --
obs0.1934 55816 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 49 203 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074908
X-RAY DIFFRACTIONf_angle_d1.0976713
X-RAY DIFFRACTIONf_dihedral_angle_d12.5611792
X-RAY DIFFRACTIONf_chiral_restr0.073783
X-RAY DIFFRACTIONf_plane_restr0.005852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.30051350.23213652X-RAY DIFFRACTION95
1.9475-2.00020.28331410.21893819X-RAY DIFFRACTION99
2.0002-2.0590.26111420.20593816X-RAY DIFFRACTION99
2.059-2.12540.25331430.20893821X-RAY DIFFRACTION99
2.1254-2.20140.24111430.19853848X-RAY DIFFRACTION99
2.2014-2.28950.23491410.19723805X-RAY DIFFRACTION99
2.2895-2.39360.25611440.20243854X-RAY DIFFRACTION99
2.3936-2.51970.24381420.20033839X-RAY DIFFRACTION99
2.5197-2.67740.22281440.20273880X-RAY DIFFRACTION99
2.6774-2.8840.21561390.19883737X-RAY DIFFRACTION96
2.884-3.17380.26191440.19973881X-RAY DIFFRACTION100
3.1738-3.63210.20291460.18583926X-RAY DIFFRACTION100
3.6321-4.57250.19221470.16523953X-RAY DIFFRACTION100
4.5725-27.15770.19931480.19473986X-RAY DIFFRACTION97

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