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- PDB-5bw2: X-ray crystal structure of Aplysia californica acetylcholine bind... -

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Basic information

Entry
Database: PDB / ID: 5bw2
TitleX-ray crystal structure of Aplysia californica acetylcholine binding protein (Ac-AChBP) Y55W in complex with 2-Pyridin-3-yl-1-aza-bicyclo[2.2.2]octane; 2-(3-pyridyl)quinuclidine; 2-PQ (TI-4699)
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / nicotine / acetylcholine
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
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
(2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
CitationJournal: To Be Published
Title: Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs
Authors: Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9299
Polymers131,1765
Non-polymers7534
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-67 kcal/mol
Surface area41080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.740, 84.400, 119.660
Angle α, β, γ (deg.)90.00, 130.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 26235.141 Da / Num. of mol.: 5 / Fragment: UNP residues 18-236 / Mutation: Y55W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK GNT1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-4VU / (2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane


Mass: 188.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.27→61.98 Å / Num. obs: 57146 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia20.3.3.3data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF 2BYN, 2BYR, 2BYS, AND 2PGZ

2byn

2byr

2bys

2pgz


Resolution: 2.27→61.98 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 2893 5.06 %
Rwork0.184 --
obs0.186 57134 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.85 Å2
Refinement stepCycle: LAST / Resolution: 2.27→61.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 56 462 8492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048330
X-RAY DIFFRACTIONf_angle_d0.73811382
X-RAY DIFFRACTIONf_dihedral_angle_d11.6662907
X-RAY DIFFRACTIONf_chiral_restr0.0271290
X-RAY DIFFRACTIONf_plane_restr0.0031469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30720.28761300.22092600X-RAY DIFFRACTION100
2.3072-2.3470.30021550.20782543X-RAY DIFFRACTION100
2.347-2.38970.2111320.21172558X-RAY DIFFRACTION100
2.3897-2.43560.28861140.20842633X-RAY DIFFRACTION100
2.4356-2.48540.32011230.2092555X-RAY DIFFRACTION100
2.4854-2.53940.29321310.22352541X-RAY DIFFRACTION100
2.5394-2.59850.23421240.20572599X-RAY DIFFRACTION100
2.5985-2.66350.26811550.20582550X-RAY DIFFRACTION100
2.6635-2.73550.23251410.20182582X-RAY DIFFRACTION100
2.7355-2.8160.2841400.19742551X-RAY DIFFRACTION100
2.816-2.90690.26371300.20692598X-RAY DIFFRACTION100
2.9069-3.01080.24641580.21172529X-RAY DIFFRACTION100
3.0108-3.13130.27451270.20612622X-RAY DIFFRACTION100
3.1313-3.27380.22161260.19872596X-RAY DIFFRACTION100
3.2738-3.44640.2391480.1872565X-RAY DIFFRACTION100
3.4464-3.66230.23091270.18252595X-RAY DIFFRACTION100
3.6623-3.9450.18791530.16582555X-RAY DIFFRACTION100
3.945-4.34190.17391370.14712601X-RAY DIFFRACTION100
4.3419-4.970.1591560.14182599X-RAY DIFFRACTION100
4.97-6.26070.20311460.1682608X-RAY DIFFRACTION100
6.2607-61.99830.19951400.18832661X-RAY DIFFRACTION100

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