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

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Basic information

Entry
Database: PDB / ID: 4oqn
TitleCrystal structure of thymidine kinase from herpes simplex virus type 1 in complex with 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-ethynyluridine / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N.W. / Scapozza, L.
Citation
Journal: To be Published
Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with EdU
Authors: Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N.W. / 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)72,8019
Polymers71,8172
Non-polymers9857
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-102 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.640, 116.280, 108.160
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
11B-512-

HOH

21B-518-

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-EDU / 2'-deoxy-5-ethynyluridine


Mass: 252.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 50.56 %
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 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.6 Å / Num. all: 32116 / Num. obs: 32116 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.092 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4592 / Rsym value: 0.343 / % possible all: 99.1

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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: 2.3→39.598 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1608 5.02 %random
Rwork0.1861 ---
obs0.1888 32041 99.62 %-
all-32061 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 61 143 4931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074908
X-RAY DIFFRACTIONf_angle_d1.0686708
X-RAY DIFFRACTIONf_dihedral_angle_d12.3621758
X-RAY DIFFRACTIONf_chiral_restr0.07780
X-RAY DIFFRACTIONf_plane_restr0.005853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.28911410.21212725X-RAY DIFFRACTION99
2.3742-2.45910.30661440.20062722X-RAY DIFFRACTION99
2.4591-2.55750.23341430.20422705X-RAY DIFFRACTION99
2.5575-2.67390.27041470.19732724X-RAY DIFFRACTION100
2.6739-2.81480.26271450.19932776X-RAY DIFFRACTION100
2.8148-2.99110.2631470.20642748X-RAY DIFFRACTION100
2.9911-3.2220.24491440.20742761X-RAY DIFFRACTION100
3.222-3.54610.26931490.19232778X-RAY DIFFRACTION100
3.5461-4.05870.23571430.16692770X-RAY DIFFRACTION100
4.0587-5.11190.16271490.15462809X-RAY DIFFRACTION100
5.1119-39.60380.23221560.18662915X-RAY DIFFRACTION100

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