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- PDB-5ke4: Crystal structure of a chimeric acetylcholine binding protein fro... -

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Basic information

Entry
Database: PDB / ID: 5ke4
TitleCrystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 6 nicotinic acetylcholine receptor in complex with 2-((5-(3,7-Diazabicyclo[3.3.1]nonan-3-yl)pyridin-3-yl)oxy)- N,N-dimethylethanamine (BPC)
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE-BINDING PROTEIN / nicotinic / acetylcholine / AChBP
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / 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
Chem-6S7 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.554 Å
AuthorsBobango, J. / Wu, J. / Talley, I.T. / Ralston, R. / Sankaran, B. / Talley, T.T.
Citation
Journal: To Be Published
Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 6 nicotinic acetylcholine receptor in complex with 2- ...Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 6 nicotinic acetylcholine receptor in complex with 2-((5-(3,7-Diazabicyclo[3.3.1]nonan-3-yl)pyridin-3-yl)oxy)- N,N-dimethylethanamine (BPC)
Authors: Bobango, J. / Wu, J. / Talley, I.T. / Ralston, R. / Sankaran, B. / Talley, T.T.
#1: Journal: Bioorg. Med. Chem. / Year: 2015
Title: The twin drug approach for novel nicotinic acetylcholine receptor ligands.
Authors: Tomassoli, I. / Gundisch, D.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release

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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)132,5229
Polymers131,3615
Non-polymers1,1624
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-72 kcal/mol
Surface area41770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.999, 118.782, 129.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 26272.174 Da / Num. of mol.: 5 / Fragment: UNP residues 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-6S7 / 2-((5-(3,7-Diazabicyclo[3.3.1]nonan-3-yl)pyridin-3-yl)oxy)-N,N-dimethylethanamine / 2-[5-[(1~{R},5~{S})-3,7-diazabicyclo[3.3.1]nonan-3-yl]pyridin-3-yl]oxy-~{N},~{N}-dimethyl-ethanamine


Mass: 290.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.1 M HEPES - Na pH 7.5, 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.554→48.299 Å / Num. obs: 41823 / % possible obs: 99.4 % / Redundancy: 14 % / Biso Wilson estimate: 40.68 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.56-2.612.40.236198.6
2.6-2.6513.70.229198.5
2.65-2.714.10.208199.1
2.7-2.7614.10.186198.9
2.76-2.8214.10.178199
2.82-2.88140.165198.9
2.88-2.9614.10.146199.1
2.96-3.04140.136199.1
3.04-3.12140.126199.3
3.12-3.23140.119199.4
3.23-3.3414.10.11199.4
3.34-3.4714.10.102199.5
3.47-3.63140.099199.7
3.63-3.8214.20.099199.8
3.82-4.0614.30.092199.9
4.06-4.3814.30.0871100
4.38-4.8214.40.0851100
4.82-5.5114.30.0851100
5.51-6.94140.0771100
6.94-5013.50.061199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.554→48.299 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.36
RfactorNum. reflection% reflection
Rfree0.2347 2008 4.81 %
Rwork0.187 --
obs0.1893 41755 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.82 Å2 / Biso mean: 39.9823 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 2.554→48.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 84 254 8387
Biso mean--41.32 38.25 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088356
X-RAY DIFFRACTIONf_angle_d0.96511432
X-RAY DIFFRACTIONf_chiral_restr0.0541304
X-RAY DIFFRACTIONf_plane_restr0.0051460
X-RAY DIFFRACTIONf_dihedral_angle_d12.3874975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5541-2.6180.28581390.2088265194
2.618-2.68880.26641430.2051280099
2.6888-2.76790.25781270.2009280699
2.7679-2.85720.32691340.2106279799
2.8572-2.95930.26821500.206281299
2.9593-3.07780.30071550.2202281199
3.0778-3.21780.26791340.2069279999
3.2178-3.38740.27631420.1982282799
3.3874-3.59960.24361490.18882851100
3.5996-3.87740.22771410.18092848100
3.8774-4.26740.19291470.15772876100
4.2674-4.88440.17861440.14362896100
4.8844-6.15190.22681450.1772917100
6.15190.20921583056100

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