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Yorodumi- PDB-6u3y: Structure-based discovery of a novel small-molecule inhibitor of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u3y | ||||||
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Title | Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus | ||||||
Components |
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Keywords | TOXIN / alpha-toxin / PVL / Leukocidins / MRSA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence. Authors: Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u3y.cif.gz | 350 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u3y.ent.gz | 285.9 KB | Display | PDB format |
PDBx/mmJSON format | 6u3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/6u3y ftp://data.pdbj.org/pub/pdb/validation_reports/u3/6u3y | HTTPS FTP |
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-Related structure data
Related structure data | 6u2sC 6u33C 6u3fC 6u3tC 6u49C 6u4pC 3b07S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 3 molecules ABD
#1: Protein | Mass: 34494.039 Da / Num. of mol.: 1 / Fragment: UNP residues 25-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: lukF-PV, hlgB_1, lukF- PV, LukPV-F, lukPV-F, lukPVF, NCTC6133_01921 Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5FBD2 |
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#2: Protein | Mass: 32374.668 Da / Num. of mol.: 2 / Fragment: UNP residues 29-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: lukS-PV, LukPV-S, lukPV-S, lukPVS, EP54_02590, EQ90_09955 Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B1Q017 |
-Non-polymers , 4 types, 376 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ACT / #6: 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: 3.17 Å3/Da / Density % sol: 61.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 6.7 mg/mL LukF-PV, 6.3 mg/mL LukS-PV, 10 mM sodium acetate, pH 5.4, 15 mM Fos-Choline-14, 40 mM beta-OG against reservoir solution of 0.16 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→38.7 Å / Num. obs: 76882 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.956 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3741 / CC1/2: 0.754 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3B07 Resolution: 2.04→38.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.954 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.19 Å2 / Biso mean: 44.123 Å2 / Biso min: 21.94 Å2
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Refinement step | Cycle: final / Resolution: 2.04→38.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.092 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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