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- PDB-8f3n: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485A va... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8f3n | ||||||
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Title | Crystal structure of Penicillin Binding Protein 5 (PBP5) T485A variant with S466 insertion 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 | ![]() | 139.1 KB | Display | ![]() |
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PDB format | ![]() | 104.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 881.9 KB | Display | ![]() |
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Full document | ![]() | 886.8 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f3fC ![]() 8f3gC ![]() 8f3hC ![]() 8f3iC ![]() 8f3jC ![]() 8f3lC ![]() 8f3mC ![]() 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: 70173.078 Da / Num. of mol.: 1 / Mutation: T485A, S466 insertion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.97 Å3/Da / Density % sol: 79.39 % |
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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 M 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: 2.99→39.24 Å / Num. obs: 34774 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.971 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.04 / Rrim(I) all: 0.137 / Χ2: 0.84 / Net I/σ(I): 13.5 / Num. measured all: 455452 |
Reflection shell | Resolution: 2.99→3.14 Å / % possible obs: 99 % / Redundancy: 13 % / Rmerge(I) obs: 0.542 / Num. measured all: 58701 / Num. unique obs: 4522 / CC1/2: 0.964 / Rpim(I) all: 0.206 / Rrim(I) all: 0.591 / Χ2: 0.6 / Net I/σ(I) obs: 2.3 |
-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: 2.99→38.2 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.09 / 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: 2.99→38.2 Å
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Refine LS restraints |
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LS refinement shell |
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