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- PDB-2mmm: Solution structure of the mature form, GK cecropin-like peptide f... -

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Basic information

Entry
Database: PDB / ID: 2mmm
TitleSolution structure of the mature form, GK cecropin-like peptide from Ae. aegypti mosquito
ComponentsK cecropin-like peptide
KeywordsANTIBIOTIC / antimicrobial peptide / Dengue Virus / Aedes aegypti / Chikungunya
Function / homologyCecropin, insect / Cecropin / Cecropin family / antibacterial humoral response / innate immune response / extracellular region / AAEL000598-PA
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsPadilla, A. / Misse, D.
CitationJournal: Plos One / Year: 2014
Title: Aedesin: structure and antimicrobial activity against multidrug resistant bacterial strains.
Authors: Godreuil, S. / Leban, N. / Padilla, A. / Hamel, R. / Luplertlop, N. / Chauffour, A. / Vittecoq, M. / Hoh, F. / Thomas, F. / Sougakoff, W. / Lionne, C. / Yssel, H. / Misse, D.
History
DepositionMar 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: K cecropin-like peptide


Theoretical massNumber of molelcules
Total (without water)3,6871
Polymers3,6871
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide K cecropin-like peptide


Mass: 3686.565 Da / Num. of mol.: 1 / Fragment: fragment 26-61 of MK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: CECD, AAEL000598 / Production host: Escherichia coli (E. coli) / References: UniProt: Q17NR1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-15N HSQC
2412D 1H-1H NOESY
1522D 1H-13C HSQC
1622D 1H-1H TOCSY
1722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.784 mM cecropin GK, 50%H2O/50%TFE50%H2O/50%TFE
20.784 mM cecropin GK, 50%D2O/50%TFE50%D2O/50%TFE
Sample
Conc. (mg/ml)ComponentSolution-ID
0.784 mMcecropin GK-11
0.784 mMcecropin GK-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.150 7.4 ambient 283 K
20.150 7.4 ambient 302 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 372 / NOE intraresidue total count: 75 / NOE long range total count: 0 / NOE medium range total count: 127 / NOE sequential total count: 142 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 26 / Protein psi angle constraints total count: 26
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.293 Å
NMR ensemble rmsDistance rms dev: 0.029 Å

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