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- PDB-4qg7: S.aureus TMK in complex with a potent inhibitor compound 18, 2-(3... -

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Basic information

Entry
Database: PDB / ID: 4qg7
TitleS.aureus TMK in complex with a potent inhibitor compound 18, 2-(3-CHLOROPHENOXY)-3-METHOXY-4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}BENZOIC ACID
ComponentsThymidylate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE/TRANSFERASE INHIBITOR kinase / thymidine monphosphate / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-32K / Thymidylate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsOlivier, N.B.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.
Authors: Kawatkar, S.P. / Keating, T.A. / Olivier, N.B. / Breen, J.N. / Green, O.M. / Guler, S.Y. / Hentemann, M.F. / Loch, J.T. / McKenzie, A.R. / Newman, J.V. / Otterson, L.G. / Martinez-Botella, G.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)47,9094
Polymers46,9092
Non-polymers1,0002
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-19 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.040, 90.450, 48.370
Angle α, β, γ (deg.)90.000, 102.100, 90.000
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: MRSA252 / Gene: SAR0483, tmk / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q6GJI9, dTMP kinase
#2: Chemical ChemComp-32K / 2-(3-chlorophenoxy)-3-methoxy-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}benzoic acid


Mass: 499.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26ClN3O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM ...Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 mM Mg2Cl 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 or compound 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
PH range: 7-8

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 17, 2010 / Details: monochrome
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→90.45 Å / Num. all: 40350 / Num. obs: 40350 / % possible obs: 89.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.04 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.761.70.3492.3513930640.34947
1.76-1.872.20.2692.91130751960.26984
1.87-22.90.2173.61649857810.21799.4
2-2.1630.1276.21616753990.12799.9
2.16-2.3630.07710.11512549890.07799.9
2.36-2.643.10.05414.11404545080.05499.9
2.64-3.053.10.04317.61255940000.04399.9
3.05-3.733.10.027271057033710.02799.7
3.73-5.283.10.0232.9793225940.0299.2
5.28-90.453.10.01822.2444814480.01898.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XDSdata reduction
AMoREphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house apostate

Resolution: 1.67→45.22 Å / Cor.coef. Fo:Fc: 0.9246 / Cor.coef. Fo:Fc free: 0.9155 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2014 5 %RANDOM
Rwork0.1873 ---
obs0.1886 40294 89.72 %-
Displacement parametersBiso max: 137.63 Å2 / Biso mean: 27.08 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.2032 Å20 Å2-10.0086 Å2
2--6.4326 Å20 Å2
3----4.2294 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.67→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 70 236 3410
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1136SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it3227HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion425SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4090SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3227HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4368HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion16.61
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3004 72 5.59 %
Rwork0.2483 1215 -
all0.2514 1287 -
obs--89.72 %

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