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Yorodumi- PDB-4hlc: Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlc | ||||||
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Title | Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Positive Thymidylate Kinase (TMK): Compound 5 | ||||||
Components | Thymidylate kinase | ||||||
Keywords | transferase/transferase inhibitor / TMK / kinase / thymidylate kinase / MRSA / pipiridine / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Boriack-Sjodin, A. / Olivier, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK). Authors: Martinez-Botella, G. / Loch, J.T. / Green, O.M. / Kawatkar, S.P. / Olivier, N.B. / Boriack-Sjodin, P.A. / Keating, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hlc.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hlc.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlc ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlc | 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 / Fragment: TMK Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: MRSA252 / Gene: SAR0483, tmk / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon + / References: UniProt: Q6GJI9, dTMP kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 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 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 23, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→42 Å / Num. all: 56013 / Num. obs: 55957 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house apo-state coordinates Resolution: 1.55→41.84 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9329 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 Details: Data reduction was accomplished by employing the AutoPROC toolbox and the structure determined by molecular replacement with AMoRE using an apo-state model of S. aureus TMK. COOT was used to ...Details: Data reduction was accomplished by employing the AutoPROC toolbox and the structure determined by molecular replacement with AMoRE using an apo-state model of S. aureus TMK. COOT was used to inspect the model and electron density and BUSTER or REFMAC were used for macromolecular refinement calculations. Geometry of the model was analyzed with MolProbity and stereochemistry of the compound analyzed with MOGUL.
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Displacement parameters | Biso mean: 26.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.175 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→41.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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