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- PDB-1i6g: NMR SOLUTION STRUCTURE OF THE INSECT-SPECIFIC NEUROTOXIN VARIANT ... -

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Basic information

Entry
Database: PDB / ID: 1i6g
TitleNMR SOLUTION STRUCTURE OF THE INSECT-SPECIFIC NEUROTOXIN VARIANT 5 (CSE-V5) FROM THE SCORPION CENTRUROIDES SCULPTURATUS EWING
ComponentsNEUROTOXIN V-5
KeywordsTOXIN / scorpion / neurotoxin / sodium channel / alpha helix / beta sheet / disulfide linkages
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
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
Alpha-like toxin CsEv5
Similarity search - Component
Biological speciesCentruroides sculpturatus (bark scorpion)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsJablonsky, M.J. / Jackson, P.L. / Krishna, N.R.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of an insect-specific neurotoxin from the New World scorpion Centruroides sculpturatus Ewing.
Authors: Jablonsky, M.J. / Jackson, P.L. / Krishna, N.R.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999SEQUENCE The authors have found that the previously published sequence (PIR C23727) was incorrect. ...SEQUENCE The authors have found that the previously published sequence (PIR C23727) was incorrect. They have demonstrated the existence of an additional Gly, 60, from sequencing, NMR, and mass spec. (Data included in the primary citation article).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROTOXIN V-5


Theoretical massNumber of molelcules
Total (without water)6,3701
Polymers6,3701
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 / 30target function
Representative

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Components

#1: Protein NEUROTOXIN V-5 / CSE-V5


Mass: 6370.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Centruroides sculpturatus (bark scorpion) / Variant: 5 / References: UniProt: P58779

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
1322D NOESY
142DQF-COSY
NMR detailsText: This structure was determined using standard homonuclear 2D-NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CsE-v5, pH 4.090% H20, 10% D2O
21mM CsE-v5, pH 4.0100% D2O
Sample conditionspH: 4.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DISNMRdisr88Brukercollection
Felix9.8Biosymprocessing
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on 1010 total restraints: 849 distance, 70 H-bonds, 91 dihedral angle
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 20

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