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- PDB-1pen: ALPHA-CONOTOXIN PNI1 -

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Basic information

Entry
Database: PDB / ID: 1pen
TitleALPHA-CONOTOXIN PNI1
ComponentsALPHA-CONOTOXIN PNIA
KeywordsNEUROTOXIN / ACETYLCHOLINE RECEPTOR / POSTSYNAPTIC / ANTAGONIST / ACETYLCHOLINE RECEPTOR INHIBITOR
Function / homologyConotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Alpha-conotoxin PnIA
Function and homology information
Biological speciesConus pennaceus (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.1 Å
AuthorsHu, S.-H. / Gehrmann, J. / Guddat, L.W. / Alewood, P.F. / Craik, D.J. / Martin, J.L.
Citation
Journal: Structure / Year: 1996
Title: The 1.1 A crystal structure of the neuronal acetylcholine receptor antagonist, alpha-conotoxin PnIA from Conus pennaceus.
Authors: Hu, S.H. / Gehrmann, J. / Guddat, L.W. / Alewood, P.F. / Craik, D.J. / Martin, J.L.
#1: Journal: J.Appl.Crystallogr. / Year: 1994
Title: Snb: Crystal Structure Determination Via Shake-and-Bake
Authors: Miller, R. / Gallo, S.M. / Khalak, H.G. / Weeks, C.M.
#2: Journal: Biochemistry / Year: 1994
Title: New Mollusc-Specific Alpha-Conotoxins Block Aplysia Neuronal Acetylcholine Receptors
Authors: Fainzilber, M. / Hasson, A. / Oren, R. / Burlingame, A.L. / Gordon, D. / Spira, M.E. / Zlotkin, E.
History
DepositionJan 29, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-CONOTOXIN PNIA


Theoretical massNumber of molelcules
Total (without water)1,6261
Polymers1,6261
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.000, 19.800, 16.500
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ALPHA-CONOTOXIN PNIA


Mass: 1625.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus pennaceus (invertebrata) / References: UniProt: P50984
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % sol: 12 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mg/mlPnIA1drop
20.1 Msodium potassium Tartrate1drop
30.05 MTris-HCl1drop
40.2 Msodium potassium Tartrate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 28, 1995
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 3459 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Num. measured all: 16298 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.14 Å / % possible obs: 80 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.1→6.1 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.152 245 10 %
Rwork0.127 --
obs0.127 2536 70 %
Displacement parametersBiso mean: 7.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.1→6.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms110 0 0 12 122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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