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- PDB-6bam: NMR solution structure of Defensin1 from Centruroides limpidus li... -

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Basic information

Entry
Database: PDB / ID: 6bam
TitleNMR solution structure of Defensin1 from Centruroides limpidus limpidus
ComponentsDefensin-1
KeywordsTOXIN / Defensin / Scorpion / Centruroides limpidus limpidus
Function / homologyInvertebrate defensins family profile. / Defensin, invertebrate/fungal / defense response to bacterium / innate immune response / extracellular region / Defensin-1
Function and homology information
Biological speciesCentruroides limpidus (Mexican scorpion)
MethodSOLUTION NMR / molecular dynamics
AuthorsEscobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Flores-Solis, D.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Direccion General de Asuntos del Personal Academico, UNAMIN207516 Mexico
CitationJournal: To Be Published
Title: From good defence into mortal risk: NMR studyand conversion of a defensin into a neurotoxin
Authors: Escobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Franco-Bodek, D. / Rodriguez-de la Vega, R. / Carrillo-Flores, E. / Rodriguez-Solano, L.A. / Flores-Solis, D. / Garaza-Garcia, A. / Titaux- ...Authors: Escobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Franco-Bodek, D. / Rodriguez-de la Vega, R. / Carrillo-Flores, E. / Rodriguez-Solano, L.A. / Flores-Solis, D. / Garaza-Garcia, A. / Titaux-Delgado, G.A. / Lopez-Vera, E. / Cano-Sanchez, P.
History
DepositionOct 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 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: Defensin-1


Theoretical massNumber of molelcules
Total (without water)3,9341
Polymers3,9341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3200 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Defensin-1 / / Cll-dlp


Mass: 3934.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Centruroides limpidus (Mexican scorpion)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q6GU94

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.2 mM M1D1, 95% H2O/5% D2O / Label: Natural abundance / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.2 mM / Component: M1D1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: .1 Not defined / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz / Details: 3mm

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.5Keller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6 / Details: version 16
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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