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- PDB-6qeu: Gga-AvBD11 (Avian beta-defensin 11 from Gallus gallus) -

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Basic information

Entry
Database: PDB / ID: 6qeu
TitleGga-AvBD11 (Avian beta-defensin 11 from Gallus gallus)
ComponentsGallinacin-11
KeywordsANTIMICROBIAL PROTEIN / new fold / double beta-defensin / defensin / avian egg
Function / homologyCCR6 chemokine receptor binding / innate immune response in mucosa / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space / Gallinacin-11
Function and homology information
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsMeudal, H. / Loth, K. / Delmas, A.F. / Landon, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure, function, and evolution ofGga-AvBD11, the archetype of the structural avian-double-beta-defensin family.
Authors: Guyot, N. / Meudal, H. / Trapp, S. / Iochmann, S. / Silvestre, A. / Jousset, G. / Labas, V. / Reverdiau, P. / Loth, K. / Herve, V. / Aucagne, V. / Delmas, A.F. / Rehault-Godbert, S. / Landon, C.
History
DepositionJan 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gallinacin-11


Theoretical massNumber of molelcules
Total (without water)9,3051
Polymers9,3051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100total energies and restraint violation statistics
RepresentativeModel #1lowest energy

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Components

#1: Protein Gallinacin-11 / Gal-11 / Beta-defensin 11 / Vitelline membrane outer layer protein 2 / Vitelline membrane outer ...Gal-11 / Beta-defensin 11 / Vitelline membrane outer layer protein 2 / Vitelline membrane outer layer protein II / VMOII


Mass: 9304.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: vitelline membrane / Tissue: egg / References: UniProt: Q6IV20

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1.08 mM [1-82]Gga-AvBD11, 90% H2O/10% D2O / Label: unlabelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.08 mM / Component: [1-82]Gga-AvBD11 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 700 MHz / Details: cryoprobe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: total energies and restraint violation statistics
Conformers calculated total number: 100 / Conformers submitted total number: 10

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