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- PDB-2y7y: APLYSIA CALIFORNICA ACHBP IN APO STATE -

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Basic information

Entry
Database: PDB / ID: 2y7y
TitleAPLYSIA CALIFORNICA ACHBP IN APO STATE
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / SECRETED / AMIDATION / CONOTOXIN
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsUlens, C. / Akdemir, A. / Jongejan, A. / van Elk, R. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / De Esch, I.J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Use of Acetylcholine Binding Protein in the Search for Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X-Ray Analysis.
Authors: Ulens, C. / Akdemir, A. / Jongejan, A. / Van Elk, R. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / De Esch, I.J.
History
DepositionFeb 2, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionMar 23, 2011ID: 2W8E
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: 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 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)123,4435
Polymers123,4435
Non-polymers00
Water20,8611158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-64.2 kcal/mol
Surface area42170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.524, 175.935, 128.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q8WSF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1158 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→52.06 Å / Num. obs: 121101 / % possible obs: 99.8 % / Observed criterion σ(I): 1.1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9T

2c9t


Resolution: 1.895→51.993 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 5598 5 %
Rwork0.1871 --
obs0.1891 112093 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.588 Å2 / ksol: 0.364 e/Å3
Refinement stepCycle: LAST / Resolution: 1.895→51.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8061 0 0 1158 9219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098542
X-RAY DIFFRACTIONf_angle_d1.19411684
X-RAY DIFFRACTIONf_dihedral_angle_d13.2073134
X-RAY DIFFRACTIONf_chiral_restr0.0871304
X-RAY DIFFRACTIONf_plane_restr0.0051523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8953-1.96310.38354830.36319371X-RAY DIFFRACTION82
1.9631-2.04170.25835100.22349473X-RAY DIFFRACTION83
2.0417-2.13460.23895390.196810436X-RAY DIFFRACTION91
2.1346-2.24710.29425300.24519980X-RAY DIFFRACTION87
2.2471-2.38790.25035290.194110324X-RAY DIFFRACTION90
2.3879-2.57230.22386050.177411078X-RAY DIFFRACTION96
2.5723-2.83120.21955610.171311309X-RAY DIFFRACTION98
2.8312-3.24080.21666080.164711415X-RAY DIFFRACTION99
3.2408-4.08280.19015770.150611520X-RAY DIFFRACTION99
4.0828-52.01280.19716560.168711589X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 25.3134 Å / Origin y: 58.1375 Å / Origin z: 5.3731 Å
111213212223313233
T0.012 Å20.0109 Å2-0.0008 Å2-0.0178 Å20.0012 Å2--0.0206 Å2
L0.3125 °2-0.0051 °2-0.0421 °2-0.4019 °20.0265 °2--0.323 °2
S-0.0057 Å °-0.0044 Å °-0.0272 Å °0.0277 Å °0.0462 Å °-0.0473 Å °-0.0032 Å °-0.0192 Å °-0.0366 Å °
Refinement TLS groupSelection details: ALL

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