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- PDB-4gsy: Crystal structure of thymidylate kinase from Staphylococcus aureu... -

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Basic information

Entry
Database: PDB / ID: 4gsy
TitleCrystal structure of thymidylate kinase from Staphylococcus aureus bound to inhibitor.
ComponentsThymidylate kinase
KeywordsTransferase/Transferase inhibitor / Transferase / nucleotide binding / thymidylate kinase activity / ATP binding / kinase activity / transferase activity / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol
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-0Y5 / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLarsen, N.A. / Olivier, N.B.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK).
Authors: Martinez-Botella, G. / Breen, J.N. / Duffy, J.E. / Dumas, J. / Geng, B. / Gowers, I.K. / Green, O.M. / Guler, S. / Hentemann, M.F. / Hernandez-Juan, F.A. / Joseph-McCarthy, D. / Kawatkar, S. ...Authors: Martinez-Botella, G. / Breen, J.N. / Duffy, J.E. / Dumas, J. / Geng, B. / Gowers, I.K. / Green, O.M. / Guler, S. / Hentemann, M.F. / Hernandez-Juan, F.A. / Joseph-McCarthy, D. / Kawatkar, S. / Larsen, N.A. / Lazari, O. / Loch, J.T. / Macritchie, J.A. / McKenzie, A.R. / Newman, J.V. / Olivier, N.B. / Otterson, L.G. / Owens, A.P. / Read, J. / Sheppard, D.W. / Keating, T.A.
History
DepositionAug 28, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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)47,9164
Polymers46,9092
Non-polymers1,0072
Water2,972165
1
A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9582
Polymers23,4551
Non-polymers5031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9582
Polymers23,4551
Non-polymers5031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.984, 90.635, 48.409
Angle α, β, γ (deg.)90.00, 102.99, 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 / Fragment: Thymidylate Kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: SA0440, SAR0483, tmk / Production host: Escherichia coli (E. coli)
References: UniProt: P65249, UniProt: Q6GJI9*PLUS, dTMP kinase
#2: Chemical ChemComp-0Y5 / 4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid


Mass: 503.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24F3N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 21-24% PEG 3350, 200 mM Mg2Cl, 100 mM PCPT buffer , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→36.89 Å / Num. all: 41271 / Num. obs: 41239 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5952 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTERrefinement
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→36.89 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 2081 5.05 %RANDOM
Rwork0.1889 ---
all0.1897 41271 --
obs0.1891 41239 --
Displacement parametersBiso mean: 32.27 Å2
Baniso -1Baniso -2Baniso -3
1--4.8023 Å20 Å2-9.651 Å2
2--6.9073 Å20 Å2
3----2.105 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.71→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 72 165 3271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.11
X-RAY DIFFRACTIONo_dihedral_angle_d17.37
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2494 140 4.68 %
Rwork0.2408 2854 -
obs-2994 97.06 %

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