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Yorodumi- PDB-6bsr: Crystal structure of penicillin-binding protein 4 (PBP4) from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bsr | |||||||||
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Title | Crystal structure of penicillin-binding protein 4 (PBP4) from Enterococcus faecalis in the benzylpenicillin bound form. | |||||||||
Components | PBP4 protein | |||||||||
Keywords | HYDROLASE / Penicillin binding protein / transpeptidase / beta-lactam / antibiotic / benzylpenicillin | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Moon, T.M. / D'Andrea, E.D. / Peti, W. / Page, R. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The structures of penicillin-binding protein 4 (PBP4) and PBP5 fromEnterococciprovide structural insights into beta-lactam resistance. Authors: Moon, T.M. / D'Andrea, E.D. / Lee, C.W. / Soares, A. / Jakoncic, J. / Desbonnet, C. / Garcia-Solache, 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 | 6bsr.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bsr.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/6bsr ftp://data.pdbj.org/pub/pdb/validation_reports/bs/6bsr | HTTPS FTP |
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-Related structure data
Related structure data | 6bsqC 6mkaC 6mkfC 6mkgC 6mkhC 6mkiC 6mkjC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 72965.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: pbp4, DRJ71_03440, FKY84_09230, KUB3007_C20250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K3C9 |
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-Non-polymers , 5 types, 400 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PNM / | #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: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 40 mM potassium phosphate monobasic, 18% PEG8000, 22% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON II / Detector: CMOS / Date: Sep 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→17.7 Å / Num. obs: 34537 / % possible obs: 99.7 % / Redundancy: 8.1 % / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.34→2.38 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→17.65 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→17.65 Å
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Refine LS restraints |
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LS refinement shell |
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