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- PDB-6mka: Crystal structure of penicillin binding protein 5 (PBP5) from Ent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mka | ||||||
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Title | Crystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the open conformation | ||||||
![]() | penicillin binding protein 5 (PBP5) | ||||||
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Function / homology | ![]() peptidoglycan L,D-transpeptidase activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moon, T.M. / Lee, C. / D'Andrea, E.D. / Peti, W. / Page, R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.1 KB | Display | ![]() |
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PDB format | ![]() | 105.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bsqC ![]() 6bsrC ![]() 6mkfC ![]() 6mkgC ![]() 6mkhC ![]() 6mkiC ![]() 6mkjC ![]() 5dvyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.56 Å3/Da / Density % sol: 77.88 % / Description: rods |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M trisodium citrate, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→39.5 Å / Num. obs: 45763 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 47.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.054 / Rrim(I) all: 0.08 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4382 / CC1/2: 0.707 / Rpim(I) all: 0.419 / Rrim(I) all: 0.613 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5DVY Resolution: 2.698→39.503 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54 / 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: 2.698→39.503 Å
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Refine LS restraints |
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LS refinement shell |
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