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- PDB-6y14: Bicyclic peptide bp65 crystallized as racemic mixture at 0.9 Angs... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y14 | |||||||||
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Title | Bicyclic peptide bp65 crystallized as racemic mixture at 0.9 Angstrom resolution | |||||||||
![]() | bp65 | |||||||||
![]() | ANTIBIOTIC / Antimicrobial / Bicyclic / Stapled | |||||||||
Function / homology | CITRIC ACID![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Baeriswyl, S. / Stocker, A. / Reymond, J.-L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #1: ![]() Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #2: ![]() Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #3: ![]() Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.6 KB | Display | ![]() |
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PDB format | ![]() | 17.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.3 KB | Display | ![]() |
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Full document | ![]() | 364.7 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 2.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y0uC ![]() 6y0vC ![]() 6y13C ![]() 6y1sC ![]() 7nefC ![]() 7newC 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/peptide | Mass: 1483.001 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Antimicrobial Bicyclic Stapled Peptide bp65, crystallized as racemate with its D-enantiomer bp69 Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 45.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 20, 2017 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→27.7 Å / Num. obs: 29455 / % possible obs: 87.71 % / Redundancy: 1.76 % / CC1/2: 0.925 / CC star: 0.98 / R split: 0.233 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.165 / Rrim(I) all: 0.233 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 0.9→0.92 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1448 / CC1/2: 0.886 / Rpim(I) all: 0.247 / Rrim(I) all: 0.349 / % possible all: 84.73 |
-Phasing
Phasing | Method: AB_INITIO |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: NONE Resolution: 0.9→27.7 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso max: 3.95 Å2 / Biso mean: 3.95 Å2 / Biso min: 3.95 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.9→27.7 Å
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Refine LS restraints |
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