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- PDB-3tmk: CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE ... -

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Basic information

Entry
Database: PDB / ID: 3tmk
TitleCRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION
ComponentsTHYMIDYLATE KINASE
KeywordsKINASE / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


UMP/dUMP kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLavie, A. / Schlichting, I. / Konrad, M. / Goody, R.S. / Brundiers, R. / Reinstein, J.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation.
Authors: Lavie, A. / Konrad, M. / Brundiers, R. / Goody, R.S. / Schlichting, I. / Reinstein, J.
History
DepositionJan 26, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _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

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
C: THYMIDYLATE KINASE
D: THYMIDYLATE KINASE
E: THYMIDYLATE KINASE
F: THYMIDYLATE KINASE
G: THYMIDYLATE KINASE
H: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,88616
Polymers197,7558
Non-polymers7,1318
Water19,6001088
1
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2214
Polymers49,4392
Non-polymers1,7832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-28 kcal/mol
Surface area19130 Å2
MethodPISA
2
C: THYMIDYLATE KINASE
D: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2214
Polymers49,4392
Non-polymers1,7832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-26 kcal/mol
Surface area18270 Å2
MethodPISA
3
E: THYMIDYLATE KINASE
F: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2214
Polymers49,4392
Non-polymers1,7832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area18600 Å2
MethodPISA
4
G: THYMIDYLATE KINASE
H: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2214
Polymers49,4392
Non-polymers1,7832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-29 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.570, 87.320, 155.020
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.865999, -0.498083, -0.044261), (-0.496296, -0.866951, 0.045671), (-0.06112, -0.017584, -0.997976)8.50608, 4.24597, 255.49323
2given(0.999111, -0.041368, 0.008137), (0.04131, 0.999121, 0.007198), (-0.008427, -0.006856, 0.999941)10.99074, 42.22878, -19.02644
3given(0.889129, -0.457156, -0.021397), (-0.456578, -0.889271, 0.027083), (-0.031409, -0.014311, -0.999404)17.18636, 50.37848, 236.46736
4given(-0.999656, 0.019956, 0.017039), (-0.020036, -0.999789, -0.004532), (0.016945, -0.004872, 0.999845)21.44378, 6.21455, -77.58885
5given(-0.888499, 0.458395, 0.021069), (0.458434, 0.888722, -0.003202), (-0.020192, 0.006814, -0.999773)18.92866, -4.69221, 177.94644
6given(-0.999993, 0.002124, 0.003092), (-0.00212, -0.999997, 0.001236), (0.003095, 0.00123, 0.999995)35.64418, 49.10461, -96.60843
7given(-0.891271, 0.453063, 0.019243), (0.452769, 0.891449, -0.017839), (-0.025236, -0.007187, -0.999656)31.33823, 41.41048, 158.80917

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Components

#1: Protein
THYMIDYLATE KINASE /


Mass: 24719.375 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00572, dTMP kinase
#2: Chemical
ChemComp-T5A / P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE


Mass: 891.354 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H30N7O23P5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1088 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growpH: 4.6 / Details: pH 4.6

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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: Feb 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→43.8 Å / Num. obs: 116451 / % possible obs: 82 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. measured all: 270178
Reflection shell
*PLUS
% possible obs: 56.9 % / Rmerge(I) obs: 0.266

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TMK

1tmk


Resolution: 2→43.8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 5401 5 %RANDOM
Rwork0.209 ---
obs0.209 101931 --
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 2→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13791 440 440 1198 15869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.64
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATP5A.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_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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