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- PDB-1bh1: STRUCTURAL STUDIES OF D-PRO MELITTIN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bh1
TitleSTRUCTURAL STUDIES OF D-PRO MELITTIN, NMR, 20 STRUCTURES
ComponentsMELITTIN
KeywordsTOXIN / HEMOLYTIC POLYPEPTIDE
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 / distance geometry
AuthorsBarnham, K.J. / Hewish, D. / Werkmeister, J. / Curtain, C. / Kirkpatrick, A. / Bartone, N. / Liu, S.T. / Norton, R. / Rivett, D.
CitationJournal: J.Protein Chem. / Year: 2002
Title: Structure and activity of D-Pro14 melittin.
Authors: Hewish, D.R. / Barnham, K.J. / Werkmeister, J.A. / Kirkpatrick, A. / Bartone, N. / Liu, S.T. / Norton, R.S. / Curtain, C. / Rivetta, D.E.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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


Theoretical massNumber of molelcules
Total (without water)2,8501
Polymers2,8501
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 / 1000LOWEST STEREOCHEMICAL AND NOE ENERGIES
RepresentativeModel #1

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Components

#1: Protein/peptide MELITTIN


Mass: 2850.495 Da / Num. of mol.: 1 / Mutation: PRO 14 REPLACED WITH D-PRO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / References: UniProt: P01501

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
141E-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D NMR SPECTROSCOPY

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Sample preparation

DetailsContents: METHANOL
Sample conditionsIonic strength: 2mM / pH: 5.2 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
DYANA1.4structure solution
X-PLOR3.8structure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: 1000 STRUCTURES WERE INITIALLY GENERATED USING THE DISTANCE GEOMETRY PROGRAM DYANA 1.4. THESE STRUCTURES WERE REFINED USING SIMULATED ANNEALING IN X-PLOR3.8 WITH THE DISTANCE GEOMETRY FORCE ...Details: 1000 STRUCTURES WERE INITIALLY GENERATED USING THE DISTANCE GEOMETRY PROGRAM DYANA 1.4. THESE STRUCTURES WERE REFINED USING SIMULATED ANNEALING IN X-PLOR3.8 WITH THE DISTANCE GEOMETRY FORCE FIELD, THEN ENERGY MINIMIZED USING THE CHARMM FORCE FIELD WITH A DISTANCE-DEPENDENT DILECTRIC. THE 20 BEST STRUCTURES BASED ON THEIR STEREOCHEMICAL AND NOE ENERGIES WERE CHOSEN FOR ANALYSIS.
NMR ensembleConformer selection criteria: LOWEST STEREOCHEMICAL AND NOE ENERGIES
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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