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- PDB-4b2u: S67, A spider venom toxin peptide from Sicarius dolichocephalus -

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Basic information

Entry
Database: PDB / ID: 4b2u
TitleS67, A spider venom toxin peptide from Sicarius dolichocephalus
ComponentsS67
KeywordsTOXIN / SPIDER VENOM PEPTIDE / ICK
Function / homologyextracellular region / U2-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: S67


Theoretical massNumber of molelcules
Total (without water)4,2571
Polymers4,2571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100TOTAL ENERGY
RepresentativeModel #7

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Components

#1: Protein/peptide S67


Mass: 4256.849 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: M1E1F0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C CT-HSQC
12113C CT-HSQC AROMATIC
131HN(CA)CB
141HNCO
151HN(CA)CO
161HN(CO)CACB
17115N HMQC
1811H NOESY (120MS)
1911H TOCSY (120MS)
1101CC(CO)NH
1111H(CCO)NH
112113C ARO NOESY (150MS)
113113C NOESY (150MS)
114115N NOESY (150MS)
115113C NOESY (120MS
1161D2O)
1171(H)CCH TOCSY
1181HACACO
119113C CT- HSQC (D2O)
120113C HSQC (D2O)
121121 MIN AFTER REHYDRATING IN D2O
122115N HMQC
123137 MIN AFTER REHYDRATING IN D2O
124115N HMQC
125154 MIN AFTER REHYDRATING IN D2O
126115N HMQC
127170 MIN AFTER REHYDRATING IN D2O
128115N HMQC
129193 MIN AFTER REHYDRATING IN D2O
130115N HMQC
1311117 MIN AFTER REHYDRATING IN D2O
132115N HMQC
1331155 MIN AFTER REHYDRATING IN D2O
134115N HMQC
1351194 MIN AFTER REHYDRATING IN D2O
136115N HMQC
1371330 MIN AFTER REHYDRATING IN D2O
138115N HMQC
1391507 MIN AFTER REHYDRATING IN D2O
140115N HMQC
141112 MIN AFTER REHYDRATING IN D2O
142115N HMQC
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
2100% D2O
Sample conditionsIonic strength: 0.02 M / pH: 6.0 / Pressure: 1.0 atm / Temperature: 310.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAvance7502

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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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