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- PDB-1onj: Crystal structure of Atratoxin-b from Chinese cobra venom of Naja atra -

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Basic information

Entry
Database: PDB / ID: 1onj
TitleCrystal structure of Atratoxin-b from Chinese cobra venom of Naja atra
ComponentsCobrotoxin b
KeywordsTOXIN / beta-turn-beta / three-finger protein
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 Å
AuthorsLou, X. / Tu, X. / Pan, G. / Xu, C. / Fan, R. / Lu, W. / Deng, W. / Rao, P. / Teng, M. / Niu, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, N-terminal sequencing, crystallization and preliminary structural determination of atratoxin-b, a short-chain alpha-neurotoxin from Naja atra venom.
Authors: Lou, X. / Tu, X. / Pan, G. / Xu, C. / Fan, R. / Lu, W. / Deng, W. / Rao, P. / Teng, M. / Niu, L.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobrotoxin b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9402
Polymers6,8441
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 49.110, 44.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cobrotoxin b / atratoxin-b


Mass: 6843.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P80958
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 1.62 Å3/Da / Density % sol: 23.42 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: ammonium sulfate, Tris-HCl, pH 8.5, EVAPORATION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.5
32.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRL / Beamline: U7B / Wavelength: 1.1516 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1516 Å / Relative weight: 1
ReflectionResolution: 1.555→16.57 Å / Num. obs: 8222 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.56→1.64 Å / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.56 Å / Num. obs: 8305 / Num. measured all: 87491 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.39

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Processing

Software
NameClassification
MAR345data collection
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.555→16.507 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.1925 841 random
Rwork0.1714 --
all-8196 -
obs-7984 -
Refinement stepCycle: LAST / Resolution: 1.555→16.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 5 84 593
Refinement
*PLUS
Highest resolution: 1.56 Å / Lowest resolution: 16.57 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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