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Yorodumi- PDB-4qg7: S.aureus TMK in complex with a potent inhibitor compound 18, 2-(3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qg7 | ||||||
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Title | S.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 | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE/TRANSFERASE INHIBITOR kinase / thymidine monphosphate / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Olivier, N.B. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qg7.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qg7.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/4qg7 ftp://data.pdbj.org/pub/pdb/validation_reports/qg/4qg7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 140 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 17, 2010 / Details: monochrome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso max: 137.63 Å2 / Biso mean: 27.08 Å2 / Biso min: 10.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.205 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→45.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.71 Å / Total num. of bins used: 20
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