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Yorodumi- PDB-8f3o: Crystal structure of Penicillin Binding Protein 5 (PBP5) R464A va... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f3o | ||||||
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Title | Crystal structure of Penicillin Binding Protein 5 (PBP5) R464A variant apo form from Enterococcus faecium | ||||||
Components | Penicillin binding protein 5Muramoylpentapeptide carboxypeptidase | ||||||
Keywords | ANTIBIOTIC / Penicillin Binding Protein 5 / Antibiotic resistance / ANTIBIOTICS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | D'Andrea, E.D. / Choy, M.S. / Schoenle, M.V. / Peti, W. / Page, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The Molecular Basis for Resistance of E. faecium PBP5 to beta-lactam Antibiotics Authors: Hunashal, Y. / Kumar, G.S. / Choy, M.S. / Da Silva Santiago, A. / D'Andrea, E.D. / Schoenle, M.V. / Arthur, M. / Rice, L.B. / Page, R. / Peti, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f3o.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f3o.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 8f3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/8f3o ftp://data.pdbj.org/pub/pdb/validation_reports/f3/8f3o | HTTPS FTP |
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-Related structure data
Related structure data | 8f3fC 8f3gC 8f3hC 8f3iC 8f3jC 8f3lC 8f3mC 8f3nC 8f3pC 8f3qC 8f3rC 8f3sC 8f3tC 8f3uC 8f3zC 8f67C 6mkaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 70029.906 Da / Num. of mol.: 1 / Mutation: R464A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pbp5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5CKR9 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.9 Å3/Da / Density % sol: 79.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.085 M Tris pH 8.0, 2.55 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.97 Å / Num. obs: 34358 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.05 / Rrim(I) all: 0.226 / Χ2: 1 / Net I/σ(I): 14.1 / Num. measured all: 684184 |
Reflection shell | Resolution: 3→3.14 Å / % possible obs: 99.7 % / Redundancy: 20.3 % / Rmerge(I) obs: 1.756 / Num. measured all: 90868 / Num. unique obs: 4471 / CC1/2: 0.747 / Rpim(I) all: 0.396 / Rrim(I) all: 1.801 / Χ2: 1.02 / Net I/σ(I) obs: 2.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MKA Resolution: 3→39.66 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 24.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.66 Å
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Refine LS restraints |
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LS refinement shell |
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