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- PDB-4gfd: Thymidylate kinase (TMK) from S. Aureus in complex with TK-666 -

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Basic information

Entry
Database: PDB / ID: 4gfd
TitleThymidylate kinase (TMK) from S. Aureus in complex with TK-666
ComponentsThymidylate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / thymidine monphosphate / soluble / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding
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
Chem-0YB / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOlivier, N.B. / Martinez-Botella, G. / Keating, T.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: In Vivo Validation of Thymidylate Kinase (TMK) with a Rationally Designed, Selective Antibacterial Compound.
Authors: Keating, T.A. / Newman, J.V. / Olivier, N.B. / Otterson, L.G. / Andrews, B. / Boriack-Sjodin, P.A. / Breen, J.N. / Doig, P. / Dumas, J. / Gangl, E. / Green, O.M. / Guler, S.Y. / Hentemann, M. ...Authors: Keating, T.A. / Newman, J.V. / Olivier, N.B. / Otterson, L.G. / Andrews, B. / Boriack-Sjodin, P.A. / Breen, J.N. / Doig, P. / Dumas, J. / Gangl, E. / Green, O.M. / Guler, S.Y. / Hentemann, M.F. / Joseph-McCarthy, D. / Kawatkar, S. / Kutschke, A. / Loch, J.T. / McKenzie, A.R. / Pradeepan, S. / Prasad, S. / Martinez-Botella, G.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)48,0784
Polymers46,9092
Non-polymers1,1692
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-19 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.100, 90.540, 48.200
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 23454.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: strain Mu50 / Gene: SA0440, tmk / Plasmid: pLH1520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P65249, UniProt: P65248*PLUS, dTMP kinase
#2: Chemical ChemComp-0YB / 2-(3-bromophenoxy)-4-{(1R)-3,3-dimethyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid


Mass: 584.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H34BrN3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 25 mM Tris/HCl, pH 8.0, 0.15 M NaCl, 1 mM DTT, 1 mM EDTA, 20% Glycerol Well solution: 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 ...Details: Protein buffer: 25 mM Tris/HCl, pH 8.0, 0.15 M NaCl, 1 mM DTT, 1 mM EDTA, 20% Glycerol Well solution: 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 mM MgCl2, using 1:1 protein:reservoir solution with the protein solution at 13 mg/mL. Crystals were harvested and soaked overnight in a solution containing 100 mM PCPT, 35% PEG 3350, 200 mM Mg2Cl and 1-2 mM TK-666 from a 100 mM DMSO stock. After soaking the crystals were cryoprotected by soaking for 15 minutes in compound-soak solution supplemented with 20% ethylene glycol. , VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 7-8

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 25, 2011
Details: Monochromator: Kohzu HLD-4 Double Crystal Crystals: Diamond(111) (2d = 4.1188 )
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.46→90.06 Å / Num. all: 66281 / Num. obs: 65022 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.93 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / Num. unique all: 9521 / % possible all: 98.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
BUSTER2.11.2refinement
PROCESSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.88 Å / Cor.coef. Fo:Fc: 0.9171 / Cor.coef. Fo:Fc free: 0.9072 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1751 5.02 %RANDOM
Rwork0.1679 ---
all0.1694 35716 --
obs0.1694 34859 97.6 %-
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--4.8301 Å20 Å2-11.8753 Å2
2--6.6461 Å20 Å2
3----1.816 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 76 276 3359
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074298HARMONIC2
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2175 160 5.25 %
Rwork0.1704 2890 -
all0.1728 3050 -
obs-3050 97.6 %

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