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- PDB-5kzu: Crystal structure of an acetylcholine binding protein from Aplysi... -

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Basic information

Entry
Database: PDB / ID: 5kzu
TitleCrystal structure of an acetylcholine binding protein from Aplysia californica (Ac-AChBP) in complex with click chemistry compound 9-[[1-[8-methyl-8-(2-phenylethyl)-8-azoniabicyclo[3.2.1]octan-3-yl]triazol-4-yl]methyl]carbazole
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-74S / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBobango, J. / Wu, J. / Talley, I.T. / Sankaran, B. / Talley, T.T.
CitationJournal: To Be Published
Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) in complex with click chemistry compound 9-[[1-[8-methyl-8-(2-phenylethyl)-8-azoniabicyclo[3.2. ...Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) in complex with click chemistry compound 9-[[1-[8-methyl-8-(2-phenylethyl)-8-azoniabicyclo[3.2.1]octan-3-yl]triazol-4-yl]methyl]carbazole
Authors: Bobango, J. / Wu, J. / Talley, I.T. / Sankaran, B. / Talley, T.T.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)132,40613
Polymers131,0615
Non-polymers1,3458
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-126 kcal/mol
Surface area43620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.330, 98.330, 268.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 26212.105 Da / Num. of mol.: 5 / Fragment: UNP residues 16-236
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-74S / 9-[[1-[8-methyl-8-(2-phenylethyl)-8-azoniabicyclo[3.2.1]octan-3-yl]triazol-4-yl]methyl]carbazole


Mass: 476.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H34N5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
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: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→79.32 Å / Num. obs: 59592 / % possible obs: 100 % / Redundancy: 27.5 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.022 / Rrim(I) all: 0.114 / Net I/σ(I): 25.5 / Num. measured all: 1638294
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) all% possible all
2.3-2.3627.60.7425.211976543350.1420.75699.9
10.29-79.3223.90.04658.5196588230.0090.04799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2474refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYR

2byr


Resolution: 2.3→79.32 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2000 3.35 %RANDOM
Rwork0.1945 107947 --
obs0.1957 59487 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.89 Å2 / Biso mean: 34.5805 Å2 / Biso min: 17.94 Å2
Refinement stepCycle: final / Resolution: 2.3→79.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8083 0 87 200 8370
Biso mean--54.22 33.94 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098384
X-RAY DIFFRACTIONf_angle_d1.21211468
X-RAY DIFFRACTIONf_chiral_restr0.0721296
X-RAY DIFFRACTIONf_plane_restr0.0061461
X-RAY DIFFRACTIONf_dihedral_angle_d3.6255270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.32910.29641410.232939944135
2.3291-2.35980.26621380.22240324170
2.3598-2.39210.24881360.213739974133
2.3921-2.42630.30371370.215339524089
2.4263-2.46250.33061390.221940494188
2.4625-2.5010.25311400.211639534093
2.501-2.5420.28591350.210939904125
2.542-2.58580.34011380.224140394177
2.5858-2.63280.23391400.229239704110
2.6328-2.68350.29661400.23239974137
2.6835-2.73830.30141380.222139904128
2.7383-2.79780.23541420.223340374179
2.7978-2.86290.26071350.208639594094
2.8629-2.93450.28521410.218440114152
2.9345-3.01380.27331340.215639964130
3.0138-3.10250.23381310.218639984129
3.1025-3.20270.2691450.2139844129
3.2027-3.31710.23841410.210340094150
3.3171-3.450.21571360.197339924128
3.45-3.6070.2181390.187740064145
3.607-3.79710.20681360.177239954131
3.7971-4.0350.21641420.170739904132
4.035-4.34650.1691410.163439994140
4.3465-4.78390.16471400.150840134153
4.7839-5.4760.1761410.164139974138
5.476-6.89860.24361370.206439984135
6.8986-79.36760.20571380.195740004138

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