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Yorodumi- PDB-6q9n: Crystal structure of PBP2a from MRSA in complex with piperacillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q9n | ||||||
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Title | Crystal structure of PBP2a from MRSA in complex with piperacillin and quinazolinone | ||||||
Components | Penicillin binding protein 2 prime | ||||||
Keywords | HYDROLASE / Penicillin Binding Protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Martinez-Caballero, S. / Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: The Quinazolinone Allosteric Inhibitor of PBP 2a Synergizes with Piperacillin and Tazobactam against Methicillin-Resistant Staphylococcus aureus. Authors: Janardhanan, J. / Bouley, R. / Martinez-Caballero, S. / Peng, Z. / Batuecas-Mordillo, M. / Meisel, J.E. / Ding, D. / Schroeder, V.A. / Wolter, W.R. / Mahasenan, K.V. / Hermoso, J.A. / Mobashery, S. / Chang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q9n.cif.gz | 270.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q9n.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 6q9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9n ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9n | HTTPS FTP |
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-Related structure data
Related structure data | 6h5oC 3zg0S S: Starting model for refinement C: citing same article (ref.) |
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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 / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 73286.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: In chain A, the Ser is attached covalently to piperacillin (PA4 residue 403) Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria) Strain: Mu50 / ATCC 700699 / Gene: mecA, SAV0041 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JPA5 #6: Sugar | ChemComp-MUR / | |
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-Non-polymers , 5 types, 99 molecules
#2: Chemical | ChemComp-QLN / | ||||
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#3: Chemical | ChemComp-JPP / | ||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CD / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 1000, sodium chloride, HEPES, cadmium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.55 Å / Num. obs: 55031 / % possible obs: 99.77 % / Redundancy: 13.1 % / Rpim(I) all: 0.032 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.5→2.58 Å / Rpim(I) all: 0.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZG0 Resolution: 2.5→49.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.785 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 70.451 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→49.55 Å
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Refine LS restraints |
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