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- PDB-4b2v: S64, a spider venom toxin peptide from Sicarius dolichocephalus -

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Basic information

Entry
Database: PDB / ID: 4b2v
TitleS64, a spider venom toxin peptide from Sicarius dolichocephalus
ComponentsS64
KeywordsTOXIN / SPIDER VENOM PEPTIDE / ICK
Function / homologyextracellular region / U1-sicaritoxin-Sdo1a
Function and homology information
Biological speciesSICARIUS DOLICHOCEPHALUS (spider)
MethodSOLUTION NMR / CNS
AuthorsLoening, N.M. / Wilson, Z.N. / Zobel-Thropp, P.A. / Binford, G.J.
CitationJournal: Plos One / Year: 2013
Title: Solution Structures of Two Homologous Venom Peptides from Sicarius Dolichocephalus
Authors: Loening, N.M. / Wilson, Z.N. / Zobel-Thropp, P.A. / Binford, G.J.
History
DepositionJul 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S64


Theoretical massNumber of molelcules
Total (without water)3,5701
Polymers3,5701
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 / 100TOTAL ENERGY
RepresentativeModel #4

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Components

#1: Protein/peptide S64


Mass: 3570.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SICARIUS DOLICHOCEPHALUS (spider)
Description: TRANSCRIPT IDENTIFIED FROM CDNA LIBRARY CONSTRUCTED FROM VENOM GLAND MRNA
Organ: VENOM GLAND / Plasmid: PLICC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1E1F1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HMQC
1211H NOESY
1311H TOCSY
141CCCONNH
151HBHACONNH
161HCCONNH
171HN(CA)CB
181HN(CA)CO
191HNCO
1101HN(CO)CACB
111113C CT- HSQC2
112113C HSQC-NOESY
113113C HSQC2
114115N HMQC2
115115N HSQC- NOESY
11611H NOESY (100MS)
11711H TOCSY (75MS)
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED SAMPLES. STRUCTURES CREATED BY ARIA2 WITH WATER REFINEMENT.

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Sample preparation

Details
Solution-IDContents
195% H2O/5% D2O
295% H20/5% D2O
Sample conditionsIonic strength: 0.02 M / pH: 7.4 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7501
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CCPNMR ANALYSIS2.2structure solution
TALOSPLUS 3.60F13.60F1structure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE PLOS ONE CITATION ABOVE.
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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