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- PDB-1p72: Crystal structure of EHV4-TK complexed with Thy and ADP -

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Basic information

Entry
Database: PDB / ID: 1p72
TitleCrystal structure of EHV4-TK complexed with Thy and ADP
ComponentsThymidine kinase
KeywordsTRANSFERASE / P-loop / Lid
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
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE / Thymidine kinase
Similarity search - Component
Biological speciesEquid herpesvirus 4 (Equine herpesvirus 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A.
CitationJournal: Structure / Year: 2003
Title: Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.
Authors: Gardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)76,23015
Polymers74,0272
Non-polymers2,20313
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-158 kcal/mol
Surface area24780 Å2
MethodPISA
2
B: Thymidine kinase
hetero molecules

B: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,46030
Polymers148,0534
Non-polymers4,40726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area13170 Å2
ΔGint-231 kcal/mol
Surface area52310 Å2
MethodPISA
3
A: Thymidine kinase
B: Thymidine kinase
hetero molecules

A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,46030
Polymers148,0534
Non-polymers4,40726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area17480 Å2
ΔGint-334 kcal/mol
Surface area48010 Å2
MethodPISA
4
B: Thymidine kinase
hetero molecules

B: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,46030
Polymers148,0534
Non-polymers4,40726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area11830 Å2
ΔGint-229 kcal/mol
Surface area53660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.301, 121.014, 118.808
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: 37013.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equid herpesvirus 4 (Equine herpesvirus 4)
Genus: Varicellovirus / Strain: 1942 / Gene: TK / Plasmid: pUT699 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C41 (DE3) / References: UniProt: P24425, thymidine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, MES, Dioxane , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES1reservoirpH6.5
21.2 Mammonium sulfate1reservoir
35 %dioxane1reservoir
45.5 mg/mlenzyme1drop
51.0 mMTMP1drop
62.0 mMADP1drop
725 mMHEPES1droppH7.0
85 mM1dropMgSO4
95 mMdithiothreitol1drop
10100 mM1dropKCl
115 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 47461
Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 242846 / % possible obs: 96.8 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VTK with unconserved residues modified to alanine

1vtk


Resolution: 2.1→29.7 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.278 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23175 4541 9.9 %RANDOM
Rwork0.18418 ---
all0.18886 41415 --
obs0.18886 41415 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.256 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---0.42 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 133 443 5585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9767150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023885
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2476
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7181.53246
X-RAY DIFFRACTIONr_mcangle_it1.32925208
X-RAY DIFFRACTIONr_scbond_it1.95331996
X-RAY DIFFRACTIONr_scangle_it3.044.51942
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 334
Rwork0.2 3048
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.343

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