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- PDB-6dst: Recombinant melittin -

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Basic information

Entry
Database: PDB / ID: 6dst
TitleRecombinant melittin
ComponentsMelittin
KeywordsTOXIN / Hemolytic / Antibacterial / Alpha-helical peptide / Bee venom
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
AuthorsRamirez, L.M. / Pande, J. / Shekhtman, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM085006 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01EY010535 United States
Citation
Journal: J Phys Chem B / Year: 2019
Title: Helical Structure of Recombinant Melittin.
Authors: Ramirez, L.S. / Pande, J. / Shekhtman, A.
#1: Journal: Biochemistry / Year: 2018
Title: Nuclear Magnetic Resonance-Based Structural Characterization and Backbone Dynamics of Recombinant Bee Venom Melittin.
Authors: Ramirez, L. / Shekhtman, A. / Pande, J.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Melittin


Theoretical massNumber of molelcules
Total (without water)2,8521
Polymers2,8521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2730 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

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


Mass: 2852.487 Da / Num. of mol.: 1 / Fragment: residues 44-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: MELT / Production host: Escherichia coli (E. coli) / References: UniProt: P01501

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
311isotropic13D 1H-15N NOESY
321isotropic13D 1H-13C NOESY
231isotropic23D (H)CCH-TOCSY
242isotropic13D HNCA
252isotropic13D HN(CA)CB
361isotropic12D 1H-15N HSQC
272isotropic12D 1H-15N HSQC
381isotropic12D 1H-13C HSQC aliphatic
292isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.05 mM [U-95% 13C; U-95% 15N] melittin, 10 % v/v [U-2H] glycerol, 10 mM potassium phosphate buffer, trifluoroethanol/waterSolution contains 10% w/v deuterated glycerol (to increase viscosity), 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 713C_15N_sample1trifluoroethanol/water
solution20.050 mM [U-95% 13C; U-95% 15N] Melittin, 10 mM potassium phosphate buffer, trifluoroethanol/waterSolution contains 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7 No glycerol added13C_15N_sample2trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.05 mMmelittin[U-95% 13C; U-95% 15N]1
10 % v/vglycerol[U-2H]1
10 mMpotassium phosphate buffernatural abundance1
0.050 mMMelittin[U-95% 13C; U-95% 15N]2
10 mMpotassium phosphate buffernatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
210 mMconditions_27 1 atm298 K
310 mMconditions_17 1 atm285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II7001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Guntert, Mumenthaler and Wuthrichrefinement
CARA1.9.1Keller and Wuthrichchemical shift assignment
CARA1.9.1Keller and Wuthrichpeak picking
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 363 NOE-derived distance constraints, 252 dihedral angle restraints, and 24 lower-limit distance constraints
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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