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- PDB-2mw7: Solution NMR structure of a novel cysteine framework containing C... -

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Basic information

Entry
Database: PDB / ID: 2mw7
TitleSolution NMR structure of a novel cysteine framework containing Conus peptide Mo3964
ComponentsMo3964
KeywordsTOXIN / Conotoxin / Neuronal Ion-Channel Modulator / Animal toxins / Marine cone snails / Conus monile / M-superfamily / Neuronal voltage-gated ion-channel modulator / Disulfide bond connectivity / Heteronuclear solution NMR spectroscopy / Side-chain dihedral angles / Hydrogen bonds / Peptide conformation / Peptide scaffolds
Function / homologytoxin activity / extracellular region / Delta/kappa-conotoxin Mo3964
Function and homology information
Biological speciesConus monile (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsSarma, S.P. / Kancherla, A.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin
Authors: Kancherla, A.K. / Meesala, S. / Jorwal, P. / Palanisamy, R. / Sikdar, S.K. / Sarma, S.P.
History
DepositionOct 29, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mo3964


Theoretical massNumber of molelcules
Total (without water)3,9741
Polymers3,9741
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 / 200structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mo3964


Mass: 3974.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus monile (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0R4I952*PLUS
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D (H)CCH-COSY
11132D 1H-13C HSQC aromatic
11213D HNHA
11333D HCACO
11433D 1H-13C NOESY
11532D 1H-13C HSQC aliphatic
11622D 1H-15N HSQC
11742D 1H-15N HSQC
11823D HNHB
11913D HN(CO)HB
12013D HNCO LRA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 - 1.0 mM [U-13C; U-15N] Mo3964-1, 0.02 % sodium azide-2, 50 mM [U-100% 2H] sodium acetate-3, 90 % H2O-4, 10 % [U-100% 2H] D2O-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 - 1.0 mM [U-15N] Mo3964-6, 0.02 % sodium azide-7, 50 mM [U-100% 2H] sodium acetate-8, 90 % H2O-9, 10 % [U-100% 2H] D2O-10, 90% H2O/10% D2O90% H2O/10% D2O
30.5 - 1.0 mM [U-13C; U-15N] Mo3964-11, 0.02 % sodium azide-12, 50 mM [U-100% 2H] sodium acetate-13, 100 % [U-100% 2H] D2O-14, 100% D2O100% D2O
40.5 - 1.0 mM [U-15N] Mo3964-15, 0.02 % sodium azide-16, 50 mM [U-100% 2H] sodium acetate-17, 100 % [U-100% 2H] D2O-18, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMo3964-1[U-13C; U-15N]0.5-1.01
0.02 %sodium azide-21
50 mMsodium acetate-3[U-100% 2H]1
90 %H2O-41
10 %D2O-5[U-100% 2H]1
mMMo3964-6[U-15N]0.5-1.02
0.02 %sodium azide-72
50 mMsodium acetate-8[U-100% 2H]2
90 %H2O-92
10 %D2O-10[U-100% 2H]2
mMMo3964-11[U-13C; U-15N]0.5-1.03
0.02 %sodium azide-123
50 mMsodium acetate-13[U-100% 2H]3
100 %D2O-14[U-100% 2H]3
mMMo3964-15[U-15N]0.5-1.04
0.02 %sodium azide-164
50 mMsodium acetate-17[U-100% 2H]4
100 %D2O-18[U-100% 2H]4
Sample conditionsIonic strength: 0.050 / pH: 5.35 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
VnmrJ3.2Variandata acquisition
Analysis2.1.5CCPNchemical shift assignment
Analysis2.1.5CCPNdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure visualization and analysis
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
UCSF Chimera1.9Eric F Pettersenstructure visualization and analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: The refinement of structures in explicit water using CNS-1.3 was set up with the help of the script WaterRefCNS
NMR constraintsProtein chi angle constraints total count: 18 / Protein other angle constraints total count: 1 / Protein phi angle constraints total count: 32 / Protein psi angle constraints total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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