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- PDB-2jqc: A L-amino acid mutant of a D-amino acid containing conopeptide -

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Basic information

Entry
Database: PDB / ID: 2jqc
TitleA L-amino acid mutant of a D-amino acid containing conopeptide
ComponentsL-mr12
KeywordsTOXIN / M cono-toxin / mr12 / NMR solution structure
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / toxin activity / extracellular region / Conomarphin-Mr3
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsHuang, F. / Du, W. / Han, Y. / Wang, C. / Chi, 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
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_software ...pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-mr12


Theoretical massNumber of molelcules
Total (without water)1,9341
Polymers1,9341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide L-mr12


Mass: 1934.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide is naturally found in Conus marmoreus. / Source: (synth.) synthetic construct (others)

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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
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM M cono-toxin mr12 mutant, 90% H2O/10% D2O90% H2O/10% D2O
22.0 mM M cono-toxin mr12 mutant, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.0 mMM cono-toxin mr12 mutant1
2.0 mMM cono-toxin mr12 mutant2
Sample conditionspH: 3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
TopSpin1.3BBruker Biospinprocessing
Sparky3.113Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
RefinementMethod: molecular dynamics / 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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