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- PDB-1akg: ALPHA-CONOTOXIN PNIB FROM CONUS PENNACEUS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1akg
TitleALPHA-CONOTOXIN PNIB FROM CONUS PENNACEUS
ComponentsALPHA-CONOTOXIN PNIB
KeywordsACETYLCHOLINE RECEPTOR ANTAGONIST / ALPHA-CONOTOXIN
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
Alpha-conotoxin PnIB
Similarity search - Component
Biological speciesConus pennaceus (invertebrata)
MethodX-RAY DIFFRACTION / DIRECT METHOD / Resolution: 1.1 Å
AuthorsHu, S.-H. / Martin, J.L.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure at 1.1 A resolution of alpha-conotoxin PnIB: comparison with alpha-conotoxins PnIA and GI.
Authors: Hu, S.H. / Gehrmann, J. / 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.
History
DepositionMay 18, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 10, 2015Group: Source and taxonomy
Revision 1.4Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: ALPHA-CONOTOXIN PNIB


Theoretical massNumber of molelcules
Total (without water)1,6411
Polymers1,6411
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)14.600, 26.100, 29.200
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/peptide ALPHA-CONOTOXIN PNIB


Mass: 1640.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BIOLOGICALLY ACTIVE MOLECULE / Source: (synth.) Conus pennaceus (invertebrata) / References: UniProt: P50985
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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 Matthews: 1.6 Å3/Da / Density % sol: 24 %
Crystal growpH: 7 / Details: 1.0 M NA FORMATE, pH 7.0
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlPnIB1drop
21.0 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRROR-FOCUSSED
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: 4483 / % possible obs: 91.5 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Biso Wilson estimate: 6 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.9
Reflection shellResolution: 1.1→1.2 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.311 / % possible all: 74
Reflection
*PLUS
Num. measured all: 39641 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Lowest resolution: 1.14 Å / % possible obs: 73.8 % / Rmerge(I) obs: 0.311

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHAKE-N-BAKEmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
SHAKE-N-BAKEphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: DIRECT METHOD / Resolution: 1.1→6 Å / Rfactor Rfree error: 0.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.157 351 10 %RANDOM
Rwork0.147 ---
obs0.147 3370 70 %-
Displacement parametersBiso mean: 7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.15 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms111 0 0 23 134
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
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_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it1.42
X-RAY DIFFRACTIONx_scbond_it1.72
X-RAY DIFFRACTIONx_scangle_it1.42.5
LS refinement shellResolution: 1.1→1.15 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.185 18 3 %
Rwork0.239 167 -
obs--31 %
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1TOPH19.PEP
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3TOPHCSDX.PROPARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 4365 / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.239

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