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Yorodumi- PDB-8f3g: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485M va... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f3g | ||||||
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Title | Crystal structure of Penicillin Binding Protein 5 (PBP5) T485M variant in the penicillin bound form from Enterococcus faecium | ||||||
Components | Penicillin binding protein 5 | ||||||
Keywords | ANTIBIOTIC / Penicillin binding / antibiotic resistance | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.59 Å | ||||||
Authors | D'Andrea, E.D. / Choy, M.S. / Schoenle, M.V. / Page, R. / Peti, W. | ||||||
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 | 8f3g.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f3g.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 8f3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f3g_validation.pdf.gz | 818.5 KB | Display | wwPDB validaton report |
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Full document | 8f3g_full_validation.pdf.gz | 823.1 KB | Display | |
Data in XML | 8f3g_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 8f3g_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/8f3g ftp://data.pdbj.org/pub/pdb/validation_reports/f3/8f3g | HTTPS FTP |
-Related structure data
Related structure data | 8f3fC 8f3hC 8f3iC 8f3jC 8f3lC 8f3mC 8f3nC 8f3oC 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: 70146.117 Da / Num. of mol.: 1 / Mutation: T485M 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-PNM / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.92 Å3/Da / Density % sol: 79.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M Citric acid pH 4.0, 2.2 M ammonium sulfate / Temp details: Room temperature |
-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: 3.59→39.7 Å / Num. obs: 20327 / % possible obs: 99.6 % / Redundancy: 19.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.306 / Rpim(I) all: 0.07 / Rrim(I) all: 0.314 / Χ2: 1 / Net I/σ(I): 10.1 / Num. measured all: 395796 |
Reflection shell | Resolution: 3.59→3.93 Å / % possible obs: 98.7 % / Redundancy: 19.5 % / Rmerge(I) obs: 2.147 / Num. measured all: 91876 / Num. unique obs: 4714 / CC1/2: 0.796 / Rpim(I) all: 0.491 / Rrim(I) all: 2.203 / Χ2: 1.04 / Net I/σ(I) obs: 2.2 |
-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: 3.59→38.12 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.39 / 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: 3.59→38.12 Å
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Refine LS restraints |
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LS refinement shell |
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