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- PDB-5mas: Peptaibol Bergofungin A -

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Basic information

Entry
Database: PDB / ID: 5mas
TitlePeptaibol Bergofungin A
ComponentsBergofungin A
KeywordsANTIBIOTIC / 3(10)-helix / peptaibols / antibiotic peptides / alpha-helix
Function / homologyBergofungin A
Function and homology information
Biological speciesEmericellopsis donezkii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.84 Å
AuthorsGessmann, R. / Petratos, K.
CitationJournal: 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
DepositionNov 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bergofungin A


Theoretical massNumber of molelcules
Total (without water)1,5101
Polymers1,5101
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-1 kcal/mol
Surface area1600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.275, 8.932, 24.604
Angle α, β, γ (deg.)90.00, 119.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Bergofungin A


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.38 % / Description: tiny hair
Crystal growTemperature: 293 K / Method: evaporation / Details: methanol/water

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 0.84→0.94 Å / Redundancy: 0.94 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.72 / % possible all: 52.8

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Processing

Software
NameVersionClassification
SHELXL2014/3refinement
XDSdata reduction
SHELXS2013/1phasing
SCALAdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.131 660 5 %THIN RESOLUTION SHELLS
all0.104 12250 --
obs0.103 11590 84.3 %-
Solvent computationSolvent model: PLATON SQUEEZE
Refine analyzeOccupancy sum hydrogen: 120 / Occupancy sum non hydrogen: 108.5
Refinement stepCycle: LAST / Resolution: 0.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms108 0 0 1 109

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