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- PDB-1a0m: 1.1 ANGSTROM CRYSTAL STRUCTURE OF A-CONOTOXIN [TYR15]-EPI -

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Basic information

Entry
Database: PDB / ID: 1a0m
Title1.1 ANGSTROM CRYSTAL STRUCTURE OF A-CONOTOXIN [TYR15]-EPI
ComponentsALPHA-CONOTOXIN [TYR15]-EPI
KeywordsACETYLCHOLINE RECEPTOR ANTAGONIST / A-CONOTOXIN / NEUROTOXIN
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 episcopatus (invertebrata)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.1 Å
AuthorsHu, S.-H. / Loughnan, M. / Miller, R. / Weeks, C.M. / Blessing, R.H. / Alewood, P.F. / Lewis, R.J. / Martin, J.L.
CitationJournal: Biochemistry / Year: 1998
Title: The 1.1 A resolution crystal structure of [Tyr15]EpI, a novel alpha-conotoxin from Conus episcopatus, solved by direct methods.
Authors: Hu, S.H. / Loughnan, M. / Miller, R. / Weeks, C.M. / Blessing, R.H. / Alewood, P.F. / Lewis, R.J. / Martin, J.L.
History
DepositionDec 3, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-CONOTOXIN [TYR15]-EPI
B: ALPHA-CONOTOXIN [TYR15]-EPI


Theoretical massNumber of molelcules
Total (without water)3,5822
Polymers3,5822
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.400, 44.400, 23.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein/peptide ALPHA-CONOTOXIN [TYR15]-EPI


Mass: 1791.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus episcopatus (invertebrata) / References: UniProt: P56638
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.6 Å3/Da / Density % sol: 24 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
Conc.: 15 mg/ml / Common name: peptide

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 27, 1996 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 9265 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 87
Reflection
*PLUS
Num. measured all: 38406
Reflection shell
*PLUS
% possible obs: 87 % / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SHAKE-N-BAKEmodel building
X-PLOR3.1refinement
SCALEPACKdata scaling
SHAKE-N-BAKEphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.1→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: ANISOTROPIC B-FACTOR REFINEMENT PERFORMED WITH SHELXL-97 GIVES AN R-FACTOR OF 13.4% AND AN R-FREE OF 0.154.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 870 10 %RANDOM
Rwork0.161 ---
obs0.161 8281 88.1 %-
Displacement parametersBiso mean: 10.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms242 0 2 42 286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.1→1.15 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.251 84 7.2 %
Rwork0.253 632 -
obs--61.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.253

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