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- PDB-1iq9: crystal structure at 1.8 A of toxin a from Naja nigricollis venom -

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Basic information

Entry
Database: PDB / ID: 1iq9
Titlecrystal structure at 1.8 A of toxin a from Naja nigricollis venom
Componentsalpha-neurotoxin
KeywordsTOXIN / neurotoxin / three fingers fold
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 nigricollis (spitting cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMenez, R. / Le Du, M.H. / Menez, A.
CitationJournal: Protein Sci. / Year: 2003
Title: Motions and structural variability within toxins: Implication for their use as scaffolds for protein engineering
Authors: Gilquin, B. / Bourgoin, M. / Menez, R. / Le Du, M.H. / Servent, D. / Zinn-Justin, S. / Menez, A.
History
DepositionJul 10, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9022
Polymers6,8061
Non-polymers961
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.900, 40.900, 73.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein alpha-neurotoxin / SHORT NEUROTOXIN 1


Mass: 6805.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja nigricollis (spitting cobra) / References: UniProt: P01426
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: sodium acetate, ammonium sulfate, hexane diol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
2100 mMsodium acetate1droppH4.5
3100 mMsodium acetate1reservoirpH4.5
42.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 11, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 7360 / Num. obs: 7347 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 10 % / Rsym value: 0.09 / Net I/σ(I): 20
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.17 / Num. unique all: 496 / Rsym value: 0.674 / % possible all: 88.4
Reflection
*PLUS
Num. obs: 7360 / % possible obs: 92 % / Num. measured all: 87663 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 81.2 % / Rmerge(I) obs: 0.674

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→8 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.24 368 5 %
Rwork0.19 --
all-7360 -
obs-7347 -
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms475 0 5 61 541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.035
X-RAY DIFFRACTIONp_angle_d3.081
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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