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- PDB-2mzm: The Solution Structure of the Magnesium-bound Conantokin-G -

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Basic information

Entry
Database: PDB / ID: 2mzm
TitleThe Solution Structure of the Magnesium-bound Conantokin-G
ComponentsConantokin-R1-B
KeywordsTRANSPORT PROTEIN INHIBITOR / TOXIN / NMDAR Antagonist / Metal binding protein
Function / homologyConantokin, conserved site / Conantokin family signature. / host cell postsynaptic membrane / ion channel regulator activity / toxin activity / extracellular region / metal ion binding / Conantokin Rl-B
Function and homology information
Biological speciesConus rolani (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsKunda, S. / Yuan, Y. / Balsara, R.D. / Zajicek, J. / Castellino, F.J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Hydroxyproline-induced Helical Disruption in Conantokin Rl-B Affects Subunit-selective Antagonistic Activities toward Ion Channels of N-Methyl-d-aspartate Receptors.
Authors: Kunda, S. / Yuan, Y. / Balsara, R.D. / Zajicek, J. / Castellino, F.J.
History
DepositionFeb 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
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 / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conantokin-R1-B


Theoretical massNumber of molelcules
Total (without water)2,2651
Polymers2,2651
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)10 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Conantokin-R1-B / Con-R1-B


Mass: 2265.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus rolani (invertebrata) / References: UniProt: P0DKZ0

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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-15N HSQC
1512D 1H-13C HSQC

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Sample preparation

DetailsContents: 2 mM Conantokin G, 10 mM [U-100% 2H] HEPES, 0.01 mg/mL DSS, 10 mM sodium chloride, 40 mM magnesium chloride, 5 % v/v [U-100% 2H] D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMConantokin G-11
10 mMHEPES-2[U-100% 2H]1
0.01 mg/mLDSS-31
10 mMsodium chloride-41
40 mMmagnesium chloride-51
5 v/vD2O-6[U-100% 2H]1
Sample conditionsIonic strength: 10 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardpeak picking
TopSpinBruker Biospinchemical shift assignment
TALOSCornilescu, Delaglio and Baxstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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