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- PDB-2mjr: Anoplin R5W structure in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2mjr
TitleAnoplin R5W structure in DPC micelles
ComponentsAnoplin
KeywordsANTIMICROBIAL PROTEIN / amphipathic helix
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / dodecyl 2-(trimethylammonio)ethyl phosphate / Anoplin
Function and homology information
Biological speciesAnoplius samariensis (insect)
MethodSOLUTION NMR / molecular dynamics
AuthorsUggerhoej, L. / Poulsen, T.J. / Wimmer, R.
CitationJournal: Chembiochem / Year: 2015
Title: Rational Design of Alpha-Helical Antimicrobial Peptides: Do's and Don'ts.
Authors: Uggerhj, L.E. / Poulsen, T.J. / Munk, J.K. / Fredborg, M. / Sondergaard, T.E. / Frimodt-Moller, N. / Hansen, P.R. / Wimmer, R.
History
DepositionJan 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anoplin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,03067
Polymers1,1851
Non-polymers22,84566
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Anoplin / As-183


Mass: 1184.537 Da / Num. of mol.: 1 / Mutation: R5W / Source method: obtained synthetically / Source: (synth.) Anoplius samariensis (insect) / References: UniProt: P0C005
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical...
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: C17H38NO4P
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
162pseudo-3D-inversion recovery weighted NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM anoplin, 150 mM [U-98% 2H] DODECYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE, 10 mM potassium phosphate, 2 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
23 mM anoplin, 150 mM [U-98% 2H] DODECYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE, 10 mM potassium phosphate, 2 mM sodium azide, 0-10 mM Gd(DTPA-BMA), 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
3 mManoplin-11
150 mMDODECYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE-2[U-98% 2H]1
10 mMpotassium phosphate-31
2 mMsodium azide-41
3 mManoplin-52
150 mMDODECYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE-6[U-98% 2H]2
10 mMpotassium phosphate-72
2 mMsodium azide-82
mMGd(DTPA-BMA)-90-102
Sample conditionsIonic strength: 0.015 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
YASARAYasara Biosciencesrefinement
TALOS+Cornilescu, Delaglio and Baxstructure solution
TALOS+Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: THE ORIENTATION OF THE PEPTIDE WITHIN THE MICELLE WAS DETERMINED FROM EXPERIMENTAL DATA (PARAMAGNETIC RELAXATION ENHANCEMENTS). THE RESTRAINT FILE CONTAINS DISTANCE RESTRAINTS FROM PEPTIDE ...Details: THE ORIENTATION OF THE PEPTIDE WITHIN THE MICELLE WAS DETERMINED FROM EXPERIMENTAL DATA (PARAMAGNETIC RELAXATION ENHANCEMENTS). THE RESTRAINT FILE CONTAINS DISTANCE RESTRAINTS FROM PEPTIDE ATOMS TO THE MICELLE CENTER, WHICH IS REPRESENTED AS THE PSEUDOATOM X, RESIDUE UNX. FIRST STEP: IN VACUO WITH NOVA FORCE FIELD. SECOND STEP: IN EXPLICIT SOLVENT (WATER/MICELLE) WITH YASARA FORCE FIELD.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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