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- PDB-2ny8: NMR structure of antibacterial defensin DEF-AAA from the insect a... -

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Basic information

Entry
Database: PDB / ID: 2ny8
TitleNMR structure of antibacterial defensin DEF-AAA from the insect anopheles gambiae
Componentsdefensin
KeywordsANTIMICROBIAL PROTEIN / insect defensin / CSab motif / antibacterial
Function / homology
Function and homology information


humoral immune response / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / extracellular space
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodSOLUTION NMR / simulated annealing with torsion angle space (ARIA, CNS)
AuthorsLandon, C. / Barbault, F. / Vovelle, F.
CitationJournal: Proteins / Year: 2008
Title: Rational design of peptides active against the gram positive bacteria Staphylococcus aureus
Authors: Landon, C. / Barbault, F. / Legrain, M. / Guenneugues, M. / Vovelle, F.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: defensin


Theoretical massNumber of molelcules
Total (without water)4,1481
Polymers4,1481
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)10 / 100structures with the lowest energy and the least restraint violations
RepresentativeModel #1lowest restraint energy

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Components

#1: Protein/peptide defensin / def-AAA


Mass: 4147.796 Da / Num. of mol.: 1 / Fragment: residues 63-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: DEF1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q17027
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
241DQF-COSY
2512D TOCSY
2612D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2mM anopheles defensin; 40mM sodium acetate buffer
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140mM sodium acetate buffer 4.9ambient 293 K
2440mM sodium acetate buffer 4.9ambient 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
NMRView5Johnsondata analysis
ARIA1.1Linge & Nilgesstructure solution
CNS1.1brungerstructure solution
CNS1.1brungerrefinement
RefinementMethod: simulated annealing with torsion angle space (ARIA, CNS)
Software ordinal: 1
Details: the structures are based on a total of 627 NOE-derived distance constraints
NMR representativeSelection criteria: lowest restraint energy
NMR ensembleConformer selection criteria: structures with the lowest energy and the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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