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- PDB-1tmk: YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP) -

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Basic information

Entry
Database: PDB / ID: 1tmk
TitleYEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP)
ComponentsTHYMIDYLATE KINASE
KeywordsPHOSPHOTRANSFERASE / TRANSFERASE (PHOSPHOTRANSFERASE) / KINASE / THYMIDINE ACTIVATION PATHWAY / ENZYME
Function / homology
Function and homology information


: / Interconversion of nucleotide di- and triphosphates / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SIR WITH NCS / Resolution: 2.1 Å
AuthorsLavie, A. / Schlichting, I.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.
Authors: Lavie, A. / Vetter, I.R. / Konrad, M. / Goody, R.S. / Reinstein, J. / Schlichting, I.
History
DepositionJun 12, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1795
Polymers49,4392
Non-polymers7403
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-36 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.450, 141.200, 48.750
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9838, -0.1627, -0.0758), (-0.1629, -0.9866, 0.003), (-0.0753, 0.0094, -0.9971)
Vector: 3.4969, 38.2928, 8.7175)

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Components

#1: Protein THYMIDYLATE KINASE


Mass: 24719.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P00572, dTMP kinase
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.39 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5 / Details: 30% PEG 4000 100 MM HEPES PH 7.5 25 MM MGAC
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mMdTDP1drop
319 %PEG40001reservoir
425 mM1reservoirMgAc
5100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→12.67 Å / Num. obs: 25398 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.065
Reflection shellResolution: 2.1→2.14 Å / Rsym value: 0.281 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 51803 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 65.4 % / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: SIR WITH NCS / Resolution: 2.1→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1134 5 %RANDOM
Rwork0.18 ---
obs0.18 23520 88.5 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 42 5 282 3625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3238 38 5 %
Rwork0.2589 862 -
obs--65.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATMP.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.68
LS refinement shell
*PLUS
Rfactor obs: 0.2589

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