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- PDB-2tmk: YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDIN... -

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Basic information

Entry
Database: PDB / ID: 2tmk
TitleYEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)
ComponentsTHYMIDYLATE KINASE
KeywordsPHOSPHOTRANSFERASE / TRANSFERASE (PHOSPHOTRANSFERASE) / KINASE / THYMIDINE ACTIVATION PATHWAY / ENZYME / AZT
Function / homology
Function and homology information


UMP/dUMP kinase activity / Interconversion of nucleotide di- and triphosphates / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / 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
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH 1TMP / Resolution: 2.4 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 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: 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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3256
Polymers49,4392
Non-polymers8874
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-44 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.420, 144.200, 49.720
Angle α, β, γ (deg.)90.00, 110.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9866, -0.1554, -0.0491), (-0.155, -0.9878, 0.0122), (-0.0504, -0.0044, -0.9987)
Vector: 3.25, 38.54, 8.92)

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ATM / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA SULFATE ION IS MODELLED BOUND TO THE P-LOOP OF EACH MONOMER.

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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: 2.53 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: 22% PEG 5000 MME 100 MM HEPES PH 7.5 200 MM AMMONIUM SULFATE
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: 277 K
Diffraction sourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. obs: 17930 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.083 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.268 / % possible all: 89.4
Reflection
*PLUS
Num. measured all: 43762 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 89.4 % / Rmerge(I) obs: 0.268

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH 1TMP
Starting model: PDB ENTRY 1TMK

1tmk


Resolution: 2.4→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 850 5 %RANDOM
Rwork0.182 ---
obs0.182 17930 93.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 46 0 166 3518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
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: 2.4→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3322 50 5 %
Rwork0.2561 685 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNAAZT.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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