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- PDB-1f94: THE 0.97 RESOLUTION STRUCTURE OF BUCANDIN, A NOVEL TOXIN ISOLATED... -

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Basic information

Entry
Database: PDB / ID: 1f94
TitleTHE 0.97 RESOLUTION STRUCTURE OF BUCANDIN, A NOVEL TOXIN ISOLATED FROM THE MALAYAN KRAIT
ComponentsBUCANDIN
KeywordsTOXIN / three-finger snake presynaptic neurotoxin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake toxin/toxin-like / Snake toxin and toxin-like protein / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesBungarus candidus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.97 Å
AuthorsKuhn, P. / Deacon, A.M. / Comoso, S. / Rajaseger, G. / Kini, R.M. / Uson, I. / Kolatkar, P.R.
CitationJournal: 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
DepositionJul 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.970, 22.520, 32.600
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: iso-propanol, ammonium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %2-propanol1reservoir
30.1 MTris-HCl1reservoir
40.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.97→32 Å / Num. all: 33370 / Num. obs: 33370 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.9
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.66 / Num. unique all: 2329 / % possible all: 94.7
Reflection
*PLUS
Num. measured all: 119818
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHELXmodel building
SHELXL-97refinement
CCP4(SCALA)data scaling
SHELXphasing
RefinementResolution: 0.97→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1636 -5% random (with shelxpro) all reflections included on last refinement cycle
Rwork0.1237 ---
all0.1234 33339 --
obs0.1234 33339 99.6 %-
Refinement stepCycle: LAST / Resolution: 0.97→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 118 1089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d2.26
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 2.26

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