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- PDB-1p73: Crystal structure of EHV4-TK complexed with TP4A -

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Basic information

Entry
Database: PDB / ID: 1p73
TitleCrystal structure of EHV4-TK complexed with TP4A
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
Chem-4TA / Thymidine kinase
Similarity search - Component
Biological speciesEquid herpesvirus 4 (Equine herpesvirus 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,33919
Polymers148,0534
Non-polymers4,28615
Water2,648147
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,41012
Polymers74,0272
Non-polymers2,38310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9297
Polymers74,0272
Non-polymers1,9035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.347, 118.293, 122.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Thymidine kinase


Mass: 37013.301 Da / Num. of mol.: 4
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.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-4TA / P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE


Type: RNA linking / Mass: 807.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25N7O20P4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 54.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, MES, Dioxane, pH 6.5, Vapor Diffusion, Hanging drop, microseeding, temperature 298K, VAPOR DIFFUSION, HANGING DROP
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: 2.7 Å / Num. obs: 45176
Reflection
*PLUS
Num. all: 902706 / % possible obs: 98.4 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P72

1p72


Resolution: 2.7→29.68 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.846 / SU B: 13.112 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27629 4439 10 %RANDOM
Rwork0.21252 ---
all0.21889 40082 --
obs0.21889 40082 98.44 %-
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: 36.921 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å20 Å2
2---0.58 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9790 0 259 147 10196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02110257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.97514018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45151282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.24637
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5551.56425
X-RAY DIFFRACTIONr_mcangle_it1.059210255
X-RAY DIFFRACTIONr_scbond_it1.33133832
X-RAY DIFFRACTIONr_scangle_it2.2064.53758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 289
Rwork0.254 2734
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.42

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