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- PDB-4oql: Crystal structure of thymidine kinase from herpes simplex virus t... -

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Basic information

Entry
Database: PDB / ID: 4oql
TitleCrystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU
ComponentsThymidine kinase
KeywordsTRANSFERASE / DNA SYNTHESIS / THYMIDINE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / 5-ETHYNYLURIDINE NUCLEOSIDE DERIVATIVE
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
2'-deoxy-5-ethynyl-2',2'-difluorouridine / 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. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L.
Citation
Journal: To be Published
Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU
Authors: Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides.
Authors: Neef, A.B. / Luedtke, N.W.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,8739
Polymers71,8172
Non-polymers1,0577
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-107 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.385, 116.419, 108.118
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-616-

HOH

21B-504-

HOH

31B-521-

HOH

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Components

#1: Protein Thymidine kinase


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-F2U / 2'-deoxy-5-ethynyl-2',2'-difluorouridine / 2'-deoxy-2',2'-difluoro-5-ethynyluridine


Mass: 288.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10F2N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
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
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→27.42 Å / Num. all: 41988 / Num. obs: 41988 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.085 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6052 / Rsym value: 0.33 / % possible all: 99.6

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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→27.4 Å / SU ML: 0.22 / Isotropic thermal model: 22.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1988 4.74 %random
Rwork0.1781 ---
obs0.1802 41946 99.84 %-
all-41962 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 65 248 5010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084880
X-RAY DIFFRACTIONf_angle_d1.076669
X-RAY DIFFRACTIONf_dihedral_angle_d11.6271754
X-RAY DIFFRACTIONf_chiral_restr0.073775
X-RAY DIFFRACTIONf_plane_restr0.005843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.26861360.2242790X-RAY DIFFRACTION99
2.1525-2.21070.28921370.19842822X-RAY DIFFRACTION100
2.2107-2.27570.27971400.19082815X-RAY DIFFRACTION100
2.2757-2.34910.22541380.18212807X-RAY DIFFRACTION100
2.3491-2.4330.22271400.18082835X-RAY DIFFRACTION100
2.433-2.53040.2631360.18682866X-RAY DIFFRACTION100
2.5304-2.64540.25491450.18682829X-RAY DIFFRACTION100
2.6454-2.78480.25411420.18222838X-RAY DIFFRACTION100
2.7848-2.95910.2261470.19072850X-RAY DIFFRACTION100
2.9591-3.18720.20071420.18532846X-RAY DIFFRACTION100
3.1872-3.50740.2441490.17812858X-RAY DIFFRACTION100
3.5074-4.01360.20671430.1592882X-RAY DIFFRACTION100
4.0136-5.05150.16551450.14962903X-RAY DIFFRACTION100
5.0515-27.42180.20841480.18793017X-RAY DIFFRACTION100

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