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- PDB-2li7: Solution Structure of CssII -

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Basic information

Entry
Database: PDB / ID: 2li7
TitleSolution Structure of CssII
ComponentsBeta-mammal toxin Css2
KeywordsTOXIN / CssII / alfa beta scorpion toxin
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular space
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-mammal toxin Css2
Similarity search - Component
Biological speciesCentruroides suffusus suffusus (Mexican scorpion)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsno violations, model 1
Authorsdel Rio-Portilla, F. / Saucedo, A.L. / Corzo, G. / Delepierre, M. / Possani, L.D.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Solution structure of native and recombinant expressed toxin CssII from the venom of the scorpion Centruroides suffusus suffusus, and their effects on Nav1.5 Sodium channels.
Authors: Saucedo, A.L. / Del Rio-Portilla, F. / Picco, C. / Estrada, G. / Prestipino, G. / Possani, L.D. / Delepierre, M. / Corzo, G.
History
DepositionAug 24, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-mammal toxin Css2


Theoretical massNumber of molelcules
Total (without water)7,5541
Polymers7,5541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20020 structures for lowest energy and no violations
RepresentativeModel #1no violations

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Components

#1: Protein Beta-mammal toxin Css2 / Css II / CssII


Mass: 7553.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Venom
Source: (natural) Centruroides suffusus suffusus (Mexican scorpion)
Strain: CssII / References: UniProt: P08900

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the CssII, an Cs alfa/beta structure.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQFCOSY
121TOCSY
131NOESY

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Sample preparation

DetailsContents: 1.5 mM H2O, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: H2O-1
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian VXRS / Manufacturer: Varian / Model: VXRS / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
MolmolKoradi, Billeter and Wuthrichcollection
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
amberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1 / Details: Amber force field
NMR constraintsNOE constraints total: 828 / NOE intraresidue total count: 411 / NOE long range total count: 252 / NOE medium range total count: 97 / NOE sequential total count: 479
NMR representativeSelection criteria: no violations
NMR ensembleConformer selection criteria: 20 structures for lowest energy and no violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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