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- PDB-1gq0: Solution structure of Antiamoebin I, a membrane channel-forming p... -

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Basic information

Entry
Database: PDB / ID: 1gq0
TitleSolution structure of Antiamoebin I, a membrane channel-forming polypeptide; NMR, 20 structures
ComponentsANTIAMOEBIN I
KeywordsANTIBIOTIC / ANTIAMOEBIN I / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyAntiamoebin 1 / :
Function and homology information
Biological speciesEMERICELLOPSIS SP. 2723 (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsGalbraith, T.P. / Harris, R. / Driscoll, P.C. / Wallace, B.A.
Citation
Journal: Biophys. J. / Year: 2003
Title: Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide.
Authors: Galbraith, T.P. / Harris, R. / Driscoll, P.C. / Wallace, B.A.
#1: Journal: Structure / Year: 1998
Title: The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide.
Authors: Snook, C.F. / Woolley, G.A. / Oliva, G. / Pattabhi, V. / Wood, S.F. / Blundell, T.L. / Wallace, B.A.
#2: Journal: Biochim. Biophys. Acta / Year: 1998
Title: Antiamoebin can function as a carrier or as a pore-forming peptaibol.
Authors: Duclohier, H. / Snook, C.F. / Wallace, B.A.
History
DepositionNov 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIAMOEBIN I


Theoretical massNumber of molelcules
Total (without water)1,6551
Polymers1,6551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide ANTIAMOEBIN I


Type: Peptaibol / Class: Antibiotic / Mass: 1654.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ANTIAMOEBIN I IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) EMERICELLOPSIS SP. 2723 (fungus) / References: NOR: NOR00945, Antiamoebin 1
Compound detailsANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...ANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, ANTIAMOEBIN I IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: ANTIAMOEBIN I CHAIN: A COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 16 DESCRIPTION: ANTIAMOEBIN I IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Sequence detailsTHE ANTIBIOTIC REPORTED HERE IS SIMILAR IN STRUCTURE TO THAT FOUND IN EMBL:AAB11467 FROM THE ...THE ANTIBIOTIC REPORTED HERE IS SIMILAR IN STRUCTURE TO THAT FOUND IN EMBL:AAB11467 FROM THE SPECIES ACREMONIUM TUBAKII

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121ROESY
131DQF-COSY
141TOCSY
151HSQC

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Sample preparation

Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
MARDIGRASstructure solution
XPLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 246 ATOMS USED IN SIMULATED ANNEALING (INCLUDING HYDROGENS) RMSD VALUES FROM IDEAL GEOMETRY FOR 20 MODELS: BOND DISTANCES 0.013 ANGSTROMS, STANDARD DEVIATION 0.0001 BOND ANGLES 2.92 DEGREES, ...Details: 246 ATOMS USED IN SIMULATED ANNEALING (INCLUDING HYDROGENS) RMSD VALUES FROM IDEAL GEOMETRY FOR 20 MODELS: BOND DISTANCES 0.013 ANGSTROMS, STANDARD DEVIATION 0.0001 BOND ANGLES 2.92 DEGREES, STANDARD DEVIATION 0.017 IMPROPER ANGLES 6.62 DEGREES, STANDARD DEVIATION 0.028
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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