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- PDB-6evh: Lipoaminopeptide helioferin A and B from Mycogone rosea -

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Basic information

Entry
Database: PDB / ID: 6evh
TitleLipoaminopeptide helioferin A and B from Mycogone rosea
ComponentsLipoaminopeptide helioferin A and B
KeywordsANTIBIOTIC / Lipoaminopeptide / protonophoric / peptaibol / peptaibiotic
Function / homologyFLUORIDE ION
Function and homology information
Biological speciesMycogone rosea (fungus)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 0.9 Å
AuthorsGessmann, R. / Petratos, K.
CitationJournal: Acta Cryst. D / Year: 2018
Title: Aminolipopeptide helioferin A and B
Authors: Gessmann, R. / Petratos, K.
History
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoaminopeptide helioferin A and B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1763
Polymers1,1211
Non-polymers542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-3 kcal/mol
Surface area1390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.711, 10.886, 17.150
Angle α, β, γ (deg.)90.00, 93.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Lipoaminopeptide helioferin A and B


Mass: 1121.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MOO is 2-methyl-N-1-oxooctanoic acid,AMO is AHMOD is (2S, 4S, 6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoyl,AIB is alpha-aminoisobutyric acid,C9K is APAE is conformation A 2-(2-aminopropyl) ...Details: MOO is 2-methyl-N-1-oxooctanoic acid,AMO is AHMOD is (2S, 4S, 6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoyl,AIB is alpha-aminoisobutyric acid,C9K is APAE is conformation A 2-(2-aminopropyl)aminoethanol and C9N, conformation B AMAE is 2-[(2-aminopropyl)-methylamino]-ethanol
Source: (natural) Mycogone rosea (fungus)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F

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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: 1.44 Å3/Da / Description: plate, 0.5 mm x 0.2 mm x 0.03
Crystal growTemperature: 297 K / Method: evaporation / Details: slow evaporation in a closed vial

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54178 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.82→17.3 Å / Num. obs: 11314 / % possible obs: 91.5 % / Redundancy: 9.7 % / Net I/σ(I): 26.2
Reflection shellResolution: 0.9→1 Å

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Processing

Software
NameClassification
SHELXLrefinement
PROTEUM PLUSdata reduction
SAINTdata scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→17.3 Å / Cross valid method: FREE R-VALUE
Details: The last amino alcohol residue is Apae in helioferin A and Amae in helioferin B. The deposited structure is neutral The presence of a proton at N2 of the last residue Apae/Amae is implicated.
RfactorNum. reflection% reflectionSelection details
Rfree0.0932 467 5 %thin shells
Rwork0.0851 ---
obs0.0856 8673 93.3 %-
Displacement parametersBiso mean: 8 Å2
Refinement stepCycle: LAST / Resolution: 0.9→17.3 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms88 0 2 0 90

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