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- PDB-2yyf: Purification and structural characterization of a D-amino acid co... -

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Basic information

Entry
Database: PDB / ID: 2yyf
TitlePurification and structural characterization of a D-amino acid containing conopeptide, marmophine, from Conus marmoreus
ComponentsM-conotoxin mr12
KeywordsTOXIN / M-conotoxin mr12 / Mr1931
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / toxin activity / extracellular region / Conomarphin-Mr3
Function and homology information
MethodSOLUTION NMR / The structure is based on a total of 236 constraints, 226 are NOE-derived distance constraints, 8 dihedral constraints, 2 constraints from one hydrogen bonds s, using distance geometry, simulated annealing by CYANA 2.1 soft to determine the structure, and using molecular dynamics mothod to do the structurn refinement by AMBER 9.0.
AuthorsHuang, F. / Du, W. / Han, Y. / Wang, C.
CitationJournal: Febs J. / Year: 2008
Title: Purification and structural characterization of a D-amino acid-containing conopeptide, conomarphin, from Conus marmoreus.
Authors: Han, Y. / Huang, F. / Jiang, H. / Liu, L. / Wang, Q. / Wang, Y. / Shao, X. / Chi, C. / Du, W. / Wang, C.
History
DepositionApr 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M-conotoxin mr12


Theoretical massNumber of molelcules
Total (without water)1,9341
Polymers1,9341
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide M-conotoxin mr12 / Mr1931


Mass: 1934.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Conus marmoreus / References: UniProt: B2KPN7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM, 90% H2O, 10% D2O90% H2O/10% D2O
22.0mM, 99.99% D2O99.99% D2O
Sample conditionspH: 3.0 / Pressure: ambient / Temperature: 300 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
NameVersionDeveloperClassification
XwinNMR3.5Bruker Inc.collection
TopSpin1.3BBruker Inc.processing
Sparky3.11T. D. Goddard and D. G. Knellerstructure solution
CYANA2.1L. A. Systems, Inc.structure solution
Amber9refinement
RefinementMethod: The structure is based on a total of 236 constraints, 226 are NOE-derived distance constraints, 8 dihedral constraints, 2 constraints from one hydrogen bonds s, using distance geometry, ...Method: The structure is based on a total of 236 constraints, 226 are NOE-derived distance constraints, 8 dihedral constraints, 2 constraints from one hydrogen bonds s, using distance geometry, simulated annealing by CYANA 2.1 soft to determine the structure, and using molecular dynamics mothod to do the structurn refinement by AMBER 9.0.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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