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- PDB-1c01: SOLUTION STRUCTURE OF MIAMP1, A PLANT ANTIMICROBIAL PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1c01
TitleSOLUTION STRUCTURE OF MIAMP1, A PLANT ANTIMICROBIAL PROTEIN
ComponentsANTIMICROBIAL PEPTIDE 1Antimicrobial peptides
KeywordsANTIMICROBIAL PROTEIN / GREEK KEY / BETA-BARREL
Function / homology
Function and homology information


negative regulation of growth / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Antimicrobial protein MiAMP1 / MiAMP1 / Antimicrobial/protein inhibitor, gamma-crystallin-like / Gamma-B Crystallin; domain 1 - #30 / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Antimicrobial peptide 1
Similarity search - Component
Biological speciesMacadamia integrifolia (macadamia nut)
MethodSOLUTION NMR / HIGH TEMPERATURE MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsMcManus, A.M. / Nielsen, K.J. / Marcus, J.P. / Harrison, S.J. / Green, J.L. / Manners, J.M. / Craik, D.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: MiAMP1, a novel protein from Macadamia integrifolia adopts a Greek key beta-barrel fold unique amongst plant antimicrobial proteins.
Authors: McManus, A.M. / Nielsen, K.J. / Marcus, J.P. / Harrison, S.J. / Green, J.L. / Manners, J.M. / Craik, D.J.
History
DepositionJul 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIMICROBIAL PEPTIDE 1


Theoretical massNumber of molelcules
Total (without water)8,1471
Polymers8,1471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #8lowest energy

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Components

#1: Protein ANTIMICROBIAL PEPTIDE 1 / Antimicrobial peptides


Mass: 8147.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macadamia integrifolia (macadamia nut) / Organ: NUT KERNEL / References: UniProt: P80915

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
2312D NOESY
1421H-15N HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND HETERONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
11.5 MM ANTIMICROBIAL PROTEIN; 90% H2O, 10% D2O
21.5 MM ANTIMICROBIAL PROTEIN U-15N; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11.5 mM 5.0 11 atm308 K
21.5 mM 5.0 11 atm283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1BRUKERstructure solution
X-EASY1.3.7WUTHRICHstructure solution
X-PLOR3.1BRUNGERstructure solution
X-PLOR3.1BRUNGERrefinement
RefinementMethod: HIGH TEMPERATURE MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED FROM 1571 DISTANCE RESTRAINTS, 31 HYDROGEN BOND RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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