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- PDB-2lb7: Hevein-type Antifungal Peptide with a Unique 10-Cysteine Motif -

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Basic information

Entry
Database: PDB / ID: 2lb7
TitleHevein-type Antifungal Peptide with a Unique 10-Cysteine Motif
ComponentsAntimicrobial peptide 1a
KeywordsANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


chitin binding / defense response to fungus / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Endochitinase-like / Chitin recognition protein / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antimicrobial peptide 1b
Similarity search - Component
Biological speciesTriticum kiharae (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsBalashova, T.A. / Vassilevski, A.A. / Odintsova, T.I. / Grishin, E.V. / Egorov, T.A. / Arseniev, A.S.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Solution structure of a defense peptide from wheat with a 10-cysteine motif.
Authors: Dubovskii, P.V. / Vassilevski, A.A. / Slavokhotova, A.A. / Odintsova, T.I. / Grishin, E.V. / Egorov, T.A. / Arseniev, A.S.
#1: Journal: FEBS Lett. / Year: 2009
Title: A novel antifungal hevein-type peptide from Triticum kiharae seeds with a unique 10-cysteine motif
Authors: Odintsova, T.I. / Vassilevski, A.A. / Slavokhotova, A.A. / Musolyamov, A.K. / Finkina, E.I. / Khadeeva, N.V. / Rogozhin, E.A. / Korostyleva, T.V. / Pukhalsky, V.A. / Grishin, E.V. / Egorov, T.A.
History
DepositionMar 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 28, 2011Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antimicrobial peptide 1a


Theoretical massNumber of molelcules
Total (without water)4,4501
Polymers4,4501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Antimicrobial peptide 1a / WAMP-1a


Mass: 4450.060 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum kiharae (plant) / Strain: Dorof. & Migush. / Production host: Escherichia coli (E. coli) / References: UniProt: P85966

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: novel antimicrobial peptide from seeds of Triticum kiharae Dorof. et Migusch
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
2222D DQF-COSY
1312D 1H-1H TOCSY
2422D 1H-1H TOCSY
1512D 1H-1H NOESY
2622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMprotein-11
0.5 mMprotein-22
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance 1 / Manufacturer: Bruker / Model: Avance 1 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.2BRUKERcollection
TopSpin2.2BRUKERprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.chemical shift calculation
XEASYBartels et al.peak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOL2.1-2.6Koradi, Billeter and Wuthrichvisualization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 202 / Disulfide bond constraints total count: 30 / Hydrogen bond constraints total count: 60 / Protein other angle constraints total count: 0
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.12 Å / Maximum torsion angle constraint violation: 2.35 ° / Maximum upper distance constraint violation: 0.11 Å

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