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

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Basic information

Entry
Database: PDB / ID: 4oqx
TitleCrystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-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
Chem-EDV / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L.
Citation
Journal: To be Published
Title: Crystal structure of HSV1-TK complexed with Me-ARA-EdU
Authors: Neef, A.B. / Pernot, L. / Scapozza, L. / Luedkte, N.W.
#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 1.1Nov 22, 2017Group: Refinement description / Category: software
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,8299
Polymers71,8172
Non-polymers1,0137
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-102 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.420, 116.830, 108.310
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: 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-EDV / 1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione / (2'S)-2'-DEOXY-2'-METHYL-5-ETHYNYLURIDINE


Mass: 266.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 50.76 %
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: 2.5→34.9 Å / Num. all: 24367 / Num. obs: 24367 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 31.19 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.106 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3413 / Rsym value: 0.434 / % possible all: 93.9

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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: 2.5→34.871 Å / SU ML: 0.35 / Isotropic thermal model: 17.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1216 5 %random
Rwork0.1867 ---
obs0.19 24330 96.4 %-
all-24344 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 63 89 4804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084835
X-RAY DIFFRACTIONf_angle_d1.2076609
X-RAY DIFFRACTIONf_dihedral_angle_d14.0931766
X-RAY DIFFRACTIONf_chiral_restr0.077775
X-RAY DIFFRACTIONf_plane_restr0.006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60020.30781280.23382452X-RAY DIFFRACTION93
2.6002-2.71850.31320.22762462X-RAY DIFFRACTION93
2.7185-2.86170.28491270.21412502X-RAY DIFFRACTION95
2.8617-3.04090.34671350.22492532X-RAY DIFFRACTION96
3.0409-3.27560.26581320.2092586X-RAY DIFFRACTION97
3.2756-3.60490.26671370.17952590X-RAY DIFFRACTION98
3.6049-4.12580.20151410.16682620X-RAY DIFFRACTION98
4.1258-5.19530.20711360.14882629X-RAY DIFFRACTION98
5.1953-34.87480.23861480.18342741X-RAY DIFFRACTION98

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