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- PDB-8f3i: Crystal structure of Penicillin Binding Protein 5 (PBP5) S466 ins... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8f3i | ||||||
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Title | Crystal structure of Penicillin Binding Protein 5 (PBP5) S466 insertion variant penicillin bound form from Enterococcus faecium | ||||||
![]() | Penicillin binding protein 5 | ||||||
![]() | ANTIBIOTIC / Penicillin binding / antibiotic resistance / ANTIBIOTICS | ||||||
Function / homology | ![]() peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | D'Andrea, E.D. / Choy, M.S. / Schoenle, M.V. / Page, R. / Peti, W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.8 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889 KB | Display | ![]() |
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Full document | ![]() | 892.9 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f3fC ![]() 8f3gC ![]() 8f3hC ![]() 8f3jC ![]() 8f3lC ![]() 8f3mC ![]() 8f3nC ![]() 8f3oC ![]() 8f3pC ![]() 8f3qC ![]() 8f3rC ![]() 8f3sC ![]() 8f3tC ![]() 8f3uC ![]() 8f3zC ![]() 8f67C ![]() 6mkaS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 70203.102 Da / Num. of mol.: 1 / Mutation: S466 insertion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PNM / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6 Å3/Da / Density % sol: 79.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid pH 5.0, 3.0 ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→38.9 Å / Num. obs: 42818 / % possible obs: 99.7 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.031 / Rrim(I) all: 0.103 / Χ2: 0.98 / Net I/σ(I): 18.4 / Num. measured all: 475161 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible obs: 99 % / Redundancy: 11.2 % / Rmerge(I) obs: 1.049 / Num. measured all: 49018 / Num. unique obs: 4381 / CC1/2: 0.815 / Rpim(I) all: 0.323 / Rrim(I) all: 1.099 / Χ2: 0.95 / Net I/σ(I) obs: 2.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MKA Resolution: 2.8→38.9 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.63 / 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: 2.8→38.9 Å
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Refine LS restraints |
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LS refinement shell |
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