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- PDB-2ket: solution structure of BMAP-27 -

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Basic information

Entry
Database: PDB / ID: 2ket
Titlesolution structure of BMAP-27
ComponentsCathelicidin-6
KeywordsANTIBIOTIC / antimicrobial peptide / Antimicrobial / Fungicide / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 5
AuthorsYang, S. / Jung, H. / Kim, J.
CitationJournal: To be Published
Title: solution structure of BMAP-27
Authors: Yang, S. / Jung, H. / Kim, J.
History
DepositionFeb 3, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin-6


Theoretical massNumber of molelcules
Total (without water)3,2351
Polymers3,2351
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cathelicidin-6 / Antibacterial peptide BMAP-27 / Myeloid antibacterial peptide 27


Mass: 3235.142 Da / Num. of mol.: 1 / Fragment: Cathelicidin-6 domain, UNP residues 132-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P54228

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 5 mM BMAP-27-1, ethanol/water / Solvent system: ethanol/water
SampleConc.: 5 mM / Component: BMAP-27-1
Sample conditionspH: 4.3 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Developer: Brunger / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 294 / NOE intraresidue total count: 145 / NOE medium range total count: 53 / NOE sequential total count: 79
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 2.7 Å / Maximum upper distance constraint violation: 6.7 Å / Representative conformer: 5
NMR ensemble rmsDistance rms dev: 0.77 Å / Distance rms dev error: 0.22 Å

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