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- PDB-1ijc: Solution Structure of Bucandin, a Neurotoxin from the Venom of th... -

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Basic information

Entry
Database: PDB / ID: 1ijc
TitleSolution Structure of Bucandin, a Neurotoxin from the Venom of the Malayan Krait
Componentsbucandin
KeywordsTOXIN / three-finger motif / two antiparallel beta-sheets / two and four stranded beta-sheets
Function / homologyCD59 / CD59 / Snake toxin-like superfamily / Ribbon / toxin activity / extracellular region / Mainly Beta / Bucandin
Function and homology information
Biological speciesBungarus candidus (cobra)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsTorres, A.M. / Kini, R.M. / Nirthanan, S. / Kuchel, P.W.
Citation
Journal: Biochem.J. / Year: 2001
Title: NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus).
Authors: Torres, A.M. / Kini, R.M. / Selvanayagam, N. / Kuchel, P.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The atomic resolution structure of bucandin, a novel toxin isolated from the Malayan krait, determined by direct methods
Authors: Kuhn, P. / Deacon, A.M. / Comoso, S. / Rajaseger, G. / Kini, R.M. / Uson, I. / Kolatkar, P.R.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bucandin


Theoretical massNumber of molelcules
Total (without water)7,2931
Polymers7,2931
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 / 6000structures with the lowest energy
RepresentativeModel #10closest to the average

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Components

#1: Protein bucandin


Mass: 7293.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus candidus (cobra) / Secretion: VENOM / References: UniProt: P81782
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: The structures were determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.7 mM bucandin / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no salt added / pH: 3 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3.13Bartels, C., Xia T., Billeter, M., Guntert, P., Wuthrich, K.data analysis
INFITSzyperski, I., Guntert, P., Otting, G., Wuthrich, K.data analysis
NOAHMumenthaler, C., Guntert, P., Braun, W., Wuthrich, K.structure solution
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
X-PLOR3.843Brunger, A.T.structure solution
X-PLOR3.843Brunger, A.T.refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 1363 restraints, 1258 are NOE-derived distance constraints, 61 dihedral angle restraints, 44 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 6000 / Conformers submitted total number: 20

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