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- PDB-2nde: Solution Structure of Mutant of BMAP-28(1-18) -

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Basic information

Entry
Database: PDB / ID: 2nde
TitleSolution Structure of Mutant of BMAP-28(1-18)
ComponentsCathelicidin-5
KeywordsANTIMICROBIAL PROTEIN / AMP
Function / homology
Function and homology information


lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / 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 / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsAgadi, N. / Kumar, A.
CitationJournal: To be Published
Title: Structure, Function And Membrane Interaction Studies of Two Synthetic Peptides Using Solution And Solid State NMR
Authors: Agadi, N. / Kumar, A.
History
DepositionMay 12, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: Cathelicidin-5


Theoretical massNumber of molelcules
Total (without water)1,9991
Polymers1,9991
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cathelicidin-5 / Antibacterial peptide BMAP-28 / Myeloid antibacterial peptide 28


Mass: 1999.494 Da / Num. of mol.: 1 / Fragment: UNP residues 132-149 / Mutation: G1I/S5G/L11A/R12L/W14H / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P54229

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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 1H-15N HSQC
1312D 1H-13C HSQC
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 20 mM sodium phosphate-1, 10 % [U-99% 2H] D2O-2, 90 % H2O-3, 50 mM [U-99% 2H] SDS-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
10 %D2O-2[U-99% 2H]1
90 %H2O-31
50 mMSDS-4[U-99% 2H]1
Sample conditionsIonic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ASCENDBrukerASCEND7501
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
ccpnmrCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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