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Yorodumi- PDB-4m6e: The high resolution structure of tyrocidine A reveals an amphipat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m6e | ||||||
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Title | The high resolution structure of tyrocidine A reveals an amphipathic dimer | ||||||
Components | tyrocidine A | ||||||
Keywords | ANTIBIOTIC / cyclic peptide | ||||||
Function / homology | tyrocidine A / METHANOL / : Function and homology information | ||||||
Biological species | Bacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å | ||||||
Authors | Loll, P.J. / Economou, N.J. / Nahoum, V. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: The high resolution structure of tyrocidine A reveals an amphipathic dimer. Authors: Loll, P.J. / Upton, E.C. / Nahoum, V. / Economou, N.J. / Cocklin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m6e.cif.gz | 14.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m6e.ent.gz | 12 KB | Display | PDB format |
PDBx/mmJSON format | 4m6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m6e_validation.pdf.gz | 400.1 KB | Display | wwPDB validaton report |
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Full document | 4m6e_full_validation.pdf.gz | 400 KB | Display | |
Data in XML | 4m6e_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 4m6e_validation.cif.gz | 3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/4m6e ftp://data.pdbj.org/pub/pdb/validation_reports/m6/4m6e | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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/peptide | | ||
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#2: Chemical | ChemComp-MPD / ( | ||
#3: Chemical | #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: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: tyrocidine in methanol at 30 mg/mL, reservoir methanol:MPD (1:5 v/v), VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8984 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8984 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→19 Å / Num. all: 6973 / Num. obs: 6973 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 48 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.95→19 Å / SU ML: 0.05 / σ(F): 0 / Phase error: 16.57 / 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: 0.95→19 Å
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Refine LS restraints |
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LS refinement shell |
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