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Yorodumi- PDB-5m19: Crystal structure of PBP2a from MRSA in the presence of Oxacillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m19 | |||||||||
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Title | Crystal structure of PBP2a from MRSA in the presence of Oxacillin ligand | |||||||||
Components | Penicillin-binding protein 2 | |||||||||
Keywords | Penicillin binding protein / Staphylococcus aureus | |||||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / membrane Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Molina, R. / Batuecas, M.T. / Hermoso, J.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Conformational Dynamics in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus, Allosteric Communication Network and Enablement of Catalysis. Authors: Mahasenan, K.V. / Molina, R. / Bouley, R. / Batuecas, M.T. / Fisher, J.F. / Hermoso, J.A. / Chang, M. / Mobashery, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m19.cif.gz | 549.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m19.ent.gz | 450.4 KB | Display | PDB format |
PDBx/mmJSON format | 5m19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m19_validation.pdf.gz | 990.5 KB | Display | wwPDB validaton report |
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Full document | 5m19_full_validation.pdf.gz | 980.9 KB | Display | |
Data in XML | 5m19_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 5m19_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/5m19 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m19 | HTTPS FTP |
-Related structure data
Related structure data | 5m18C 5m1aC 1vqqS 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
#1: Protein | Mass: 73286.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA / Production host: Escherichia coli (E. coli) / References: UniProt: E2D9B8, UniProt: Q7DHH4*PLUS #2: Chemical | ChemComp-CD / #3: Sugar | #4: 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: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% (vol/vol) PEG 550 monomethyl ether, 880 mM NaCl, 100mMHepes (pH 7.0 buffer), and 16mMCdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.07 Å / Num. obs: 197867 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / CC1/2: 0.99 / Rsym value: 0.03 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.1 % / CC1/2: 0.94 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VQQ Resolution: 2→46.42 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 28.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.4539 Å / Origin y: -13.3062 Å / Origin z: 45.2802 Å
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Refinement TLS group |
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