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- PDB-4tmk: COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBI... -

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Basic information

Entry
Database: PDB / ID: 4tmk
TitleCOMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR TP5A
ComponentsPROTEIN (THYMIDYLATE KINASE)
KeywordsTRANSFERASE / ATP:DTMP PHOSPHOTRANSFERASE
Function / homology
Function and homology information


dTMP kinase / dTMP kinase activity / dUDP biosynthetic process / dTDP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homodimerization activity / ATP binding / cytosol / 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
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.98 Å
AuthorsLavie, A. / Ostermann, N. / Schlichting, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
Authors: Lavie, A. / Ostermann, N. / Brundiers, R. / Goody, R.S. / Reinstein, J. / Konrad, M. / Schlichting, I.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (THYMIDYLATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7202
Polymers23,8281
Non-polymers8911
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (THYMIDYLATE KINASE)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)148,31712
Polymers142,9696
Non-polymers5,3486
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area20800 Å2
ΔGint-79 kcal/mol
Surface area47550 Å2
MethodPISA
3
A: PROTEIN (THYMIDYLATE KINASE)
hetero molecules

A: PROTEIN (THYMIDYLATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4394
Polymers47,6562
Non-polymers1,7832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)151.700, 151.700, 74.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PROTEIN (THYMIDYLATE KINASE)


Mass: 23828.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A720, dTMP kinase
#2: Chemical ChemComp-T5A / P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE


Mass: 891.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N7O23P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlenzyme1drop
22 mMnucleotide1drop
31.25 Mammonium phosphate1drop
42.5 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.98→19.35 Å / Num. obs: 21854 / % possible obs: 95.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.045
Reflection
*PLUS
Num. measured all: 117407
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.136

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Processing

Software
NameVersionClassification
MLPHAREphasing
DMmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SIR / Resolution: 1.98→19.35 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: RESIDUES ARG51 AND GLN180 WERE MODELLED IN TWO ALTERNATE CONFORMATIONS. 5 ATOMS OF THE BISUBSTRATE INHIBITOR TP5A WERE MODELLED IN TWO CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1067 5 %RANDOM
Rwork0.204 ---
obs0.204 21836 95.5 %-
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 55 163 1859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.63
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.159
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: 1.98→2.07 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2983 142 4.99 %
Rwork0.261 2570 -
obs--95.4 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.63
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.159

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