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- PDB-1hje: Crystal structure of alpha-conotoxin SI -

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Basic information

Entry
Database: PDB / ID: 1hje
TitleCrystal structure of alpha-conotoxin SI
ComponentsALPHA-CONOTOXIN SI
KeywordsTOXIN / CONOTOXIN / NICOTINIC ACETYLCHOLINE RECEPTOR / VENOM
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature.
Similarity search - Domain/homology
Biological speciesCONUS STRIATUS (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.75 Å
AuthorsJanes, R.W. / Hargittai, B. / Barany, G. / Maclean, E.J. / Teat, S.J.
CitationJournal: To be Published
Title: The High Resolution Crystal Structure of Alpha-Conotoxin Si to 0.75 Angstroms
Authors: Janes, R.W. / Hargittai, B. / Barany, G. / Maclean, E.J. / Teat, S.J.
History
DepositionJan 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-CONOTOXIN SI


Theoretical massNumber of molelcules
Total (without water)1,3581
Polymers1,3581
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.092, 32.092, 14.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein/peptide ALPHA-CONOTOXIN SI / SI (2-7 / 3-13)


Mass: 1357.645 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-62 / Source method: obtained synthetically / Details: SYNTHESISED BY SOLID PHASE PEPTIDE CHEMISTRY / Source: (synth.) CONUS STRIATUS (striated cone) / References: UniProt: P15471
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALPHA-CONOTOXINS BIND TO THE NICOTINIC ACETYLCHOLINE RECEPTORS (NACHR) AND INHIBIT THEM.
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: 1.61 Å3/Da / Density % sol: 23.64 %
Crystal growDetails: 0.4M K,NA TARTRATE

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.6887
DetectorType: BRUKER AXS / Detector: CCD / Date: Jul 15, 2000
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6887 Å / Relative weight: 1
ReflectionResolution: 0.75→10.91 Å / Num. obs: 21312 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.99 % / Rsym value: 0.0612 / Net I/σ(I): 19.65
Reflection shellResolution: 0.75→0.87 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.07 / Rsym value: 0.2635 / % possible all: 96.3

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Processing

Software
NameClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.75→10.91 Å / Num. parameters: 1171 / Num. restraintsaints: 50 / σ(F): 0.5 / Details: XTALVIEW
RfactorNum. reflection% reflection
obs0.127 -97.9 %
all-133616 -
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 78 / Occupancy sum non hydrogen: 102.71
Refinement stepCycle: LAST / Resolution: 0.75→10.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91 0 0 27 118

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