+Open data
-Basic information
Entry | Database: PDB / ID: 5mas | ||||||
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Title | Peptaibol Bergofungin A | ||||||
Components | Bergofungin A | ||||||
Keywords | ANTIBIOTIC / 3(10)-helix / peptaibols / antibiotic peptides / alpha-helix | ||||||
Function / homology | Bergofungin A Function and homology information | ||||||
Biological species | Emericellopsis donezkii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.84 Å | ||||||
Authors | Gessmann, R. / Petratos, K. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution. Authors: Gessmann, R. / Axford, D. / Bruckner, H. / Berg, A. / Petratos, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mas.cif.gz | 15.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mas.ent.gz | 11.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mas_validation.pdf.gz | 406.4 KB | Display | wwPDB validaton report |
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Full document | 5mas_full_validation.pdf.gz | 406.4 KB | Display | |
Data in XML | 5mas_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 5mas_validation.cif.gz | 2.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5mas ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5mas | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1509.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NOR00964 in norine database (http://bioinfo.lifl.fr/norine/form.jsp) Source: (natural) Emericellopsis donezkii (fungus) / References: UniProt: A0A1U7Q1Y9*PLUS |
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#2: 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: 1.53 Å3/Da / Density % sol: 19.38 % / Description: tiny hair |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: methanol/water |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7293 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016 |
Radiation | Monochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7293 Å / Relative weight: 1 |
Reflection | Resolution: 0.84→30 Å / Num. obs: 12250 / % possible obs: 84.3 % / Redundancy: 1.65 % / Rmerge(I) obs: 0.095 / Rsym value: 0.09 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 0.84→0.94 Å / Redundancy: 0.94 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.72 / % possible all: 52.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.84→30 Å / Num. parameters: 985 / Num. restraintsaints: 1 / Cross valid method: FREE R-VALUE / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: PLATON SQUEEZE | ||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 120 / Occupancy sum non hydrogen: 108.5 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.84→30 Å
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