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Yorodumi- PDB-6mkf: Crystal structure of penicillin binding protein 5 (PBP5) from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mkf | ||||||
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Title | Crystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the imipenem-bound form | ||||||
Components | penicillin binding protein 5 (PBP5) | ||||||
Keywords | protein binding/antibiotic / transpeptidase / PBP / PENICILLIN-BINDING PROTEIN / protein binding-antibiotic complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Moon, T.M. / Lee, C. / 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 | 6mkf.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mkf.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/6mkf ftp://data.pdbj.org/pub/pdb/validation_reports/mk/6mkf | HTTPS FTP |
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-Related structure data
Related structure data | 6bsqC 6bsrC 6mkaC 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
#1: Protein | Mass: 69858.781 Da / Num. of mol.: 1 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: A0A075Q0W3 | ||
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#2: Chemical | ChemComp-IM2 / ( | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 6 Å3/Da / Density % sol: 79.5 % / Description: rod |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M trisodium citrate, 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2016 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings |
Radiation | Monochromator: Double crystal cryo-cooled Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.84 Å / Num. obs: 42442 / % possible obs: 99.8 % / Redundancy: 18.3 % / Biso Wilson estimate: 66.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.052 / Rrim(I) all: 0.166 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4301 / CC1/2: 0.337 / Rpim(I) all: 0.678 / Rrim(I) all: 1.803 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBP5 apo open Resolution: 2.8→29.84 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.84 Å
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Refine LS restraints |
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LS refinement shell |
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