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- PDB-1aho: THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPIO... -

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Basic information

Entry
Database: PDB / ID: 1aho
TitleTHE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN
ComponentsTOXIN II
KeywordsNEUROTOXIN / TOXIN II / SCORPION / AB INITIO PHASING
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-mammal toxin AaH2
Similarity search - Component
Biological speciesAndroctonus australis (Sahara scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.96 Å
AuthorsSmith, G.D. / Blessing, R.H. / Ealick, S.E. / Fontecilla-Camps, J.C. / Hauptman, H.A. / Housset, D. / Langs, D.A. / Miller, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Ab initio structure determination and refinement of a scorpion protein toxin.
Authors: Smith, G.D. / Blessing, R.H. / Ealick, S.E. / Fontecilla-Camps, J.C. / Hauptman, H.A. / Housset, D. / Langs, D.A. / Miller, R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of Toxin II from the Scorpion Androctonus Australis Hector Refined at 1.3 A Resolution
Authors: Housset, D. / Habersetzer-Rochat, C. / Astier, J.P. / Fontecilla-Camps, J.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Orthorhombic Crystals and Three-Dimensional Structure of the Potent Toxin II from the Scorpion Androctonus Australis Hector
Authors: Fontecilla-Camps, J.C. / Habersetzer-Rochat, C. / Rochat, H.
History
DepositionApr 8, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXIN II


Theoretical massNumber of molelcules
Total (without water)7,2621
Polymers7,2621
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.900, 40.700, 30.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TOXIN II /


Mass: 7262.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Androctonus australis (Sahara scorpion) / Strain: hector / References: UniProt: P01484
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 36.43 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: other / Details: none

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92 / Wavelength: 0.72, 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: NA
RadiationMonochromator: NA / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.721
ReflectionResolution: 0.964→16 Å / Num. obs: 31001 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 7.23 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.7
Reflection shellResolution: 0.96→0.99 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.3 / % possible all: 80
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameVersionClassification
MOSFILMdata collection
ROTAVATAdata reduction
Agrovatadata reduction
SHAKE-N-BAKEmodel building
PROFFTrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
SHAKE-N-BAKEphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.96→8 Å / σ(F): 2
Details: THE STRUCTURE WAS REFINED INITIALLY WITH X-PLOR TO A RESIDUAL OF 0.203 (25509 REFLECTIONS) AND A FREE R OF 0.224 (2830 REFLECTIONS). PROFFT (FINZEL), MODIFIED TO INCORPORATE A TWO LINE ...Details: THE STRUCTURE WAS REFINED INITIALLY WITH X-PLOR TO A RESIDUAL OF 0.203 (25509 REFLECTIONS) AND A FREE R OF 0.224 (2830 REFLECTIONS). PROFFT (FINZEL), MODIFIED TO INCORPORATE A TWO LINE WEIGHTING SCHEME (SMITH), WAS USED TO PERFORM THE FINAL REFINEMENTS INCLUDING CONTRIBUTIONS FROM HYDROGEN ATOMS. DISORDERED RESIDUES WERE IDENTIFIED GRAPHICALLY.
RfactorNum. reflection% reflection
Rwork0.158 --
all-31001 -
obs-30609 88 %
Displacement parametersBiso mean: 10.72 Å2
Refinement stepCycle: LAST / Resolution: 0.96→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 0 129 629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0110.03
X-RAY DIFFRACTIONp_mcbond_it1.1061.5
X-RAY DIFFRACTIONp_mcangle_it1.5232
X-RAY DIFFRACTIONp_scbond_it1.6921.5
X-RAY DIFFRACTIONp_scangle_it2.372
X-RAY DIFFRACTIONp_plane_restr0.0410.05
X-RAY DIFFRACTIONp_chiral_restr0.1270.15
X-RAY DIFFRACTIONp_singtor_nbd0.1920.5
X-RAY DIFFRACTIONp_multtor_nbd0.2010.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.4850.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1480.5
X-RAY DIFFRACTIONp_planar_tor4.93
X-RAY DIFFRACTIONp_staggered_tor12.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.163 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.020.022

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