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- PDB-2mw6: Structure of the bee venom toxin melittin with [(C5H5)Ru]+ fragme... -

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Basic information

Entry
Database: PDB / ID: 2mw6
TitleStructure of the bee venom toxin melittin with [(C5H5)Ru]+ fragment attached to the tryptophan residue
ComponentsMelittin
KeywordsTOXIN
Function / homology
Function and homology information


other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport / toxin activity / killing of cells of another organism / lipid binding / extracellular region
Similarity search - Function
Melittin/ Api allergen / Melittin
Similarity search - Domain/homology
Biological speciesApis mellifera (honey bee)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsPerekalin, D.S. / Pavlov, A.A. / Novikov, V.V.
CitationJournal: Chemistry / Year: 2015
Title: Selective ruthenium labeling of the tryptophan residue in the bee venom Peptide melittin.
Authors: Perekalin, D.S. / Novikov, V.V. / Pavlov, A.A. / Ivanov, I.A. / Anisimova, N.Y. / Kopylov, A.N. / Volkov, D.S. / Seregina, I.F. / Bolshov, M.A. / Kudinov, A.R.
History
DepositionOct 28, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_nmr_spectrometer ...pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 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 / 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 / _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: Melittin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1452
Polymers2,8501
Non-polymers2941
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Melittin / / Allergen Api m 3 / Allergen Api m III


Mass: 2850.495 Da / Num. of mol.: 1 / Fragment: residues 44-69 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: P01501
#2: Chemical ChemComp-3UQ / [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,4a,8a-eta)-naphthalene]ruthenium(1+)


Mass: 294.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13Ru

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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
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 6 mM Ru-melittin-1, CD3OH / Solvent system: CD3OH
SampleConc.: 6 mM / Component: Ru-melittin-1
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 298 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 software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 132
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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