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- PDB-2y56: Fragment growing induces conformational changes in acetylcholine-... -

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Basic information

Entry
Database: PDB / ID: 2y56
TitleFragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Compound 3)
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR
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-V11 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsRucktooa, P. / Edink, E. / deEsch, I.J.P. / Sixma, T.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis.
Authors: Edink, E. / Rucktooa, P. / Retra, K. / Akdemir, A. / Nahar, T. / Zuiderveld, O. / Van Elk, R. / Janssen, E. / Van Nierop, P. / Van Muijlwijk-Koezen, J. / Smit, A.B. / Sixma, T.K. / Leurs, R. / De Esch, I.J.P.
History
DepositionJan 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 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)127,70744
Polymers123,4435
Non-polymers4,26439
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-177.1 kcal/mol
Surface area44560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.930, 218.930, 218.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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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: PFASTBAC1 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-V11 / [(1S,5R)-8-[(2R)-2-HYDROXY-2-PHENYL-ETHYL]-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE


Mass: 351.439 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H25NO3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.77 Å3/Da / Density % sol: 67.36 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M MMT PH8.5, 1.1M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.282
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.59→16.05 Å / Num. obs: 20509 / % possible obs: 99.8 % / Observed criterion σ(I): 2.87 / Redundancy: 5.41 % / Biso Wilson estimate: 61.09 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.31
Reflection shellResolution: 3.59→3.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.87 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9T

2c9t


Resolution: 3.59→48.95 Å / Cor.coef. Fo:Fc: 0.9385 / Cor.coef. Fo:Fc free: 0.9204 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1027 5.01 %RANDOM
Rwork0.1738 ---
obs0.1752 20507 --
Displacement parametersBiso mean: 98.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.662 Å
Refinement stepCycle: LAST / Resolution: 3.59→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 260 0 8440
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018631HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0111779HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3821SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes225HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1205HARMONIC5
X-RAY DIFFRACTIONt_it8631HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion3.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1140SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8513SEMIHARMONIC4
LS refinement shellResolution: 3.59→3.78 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2435 139 4.68 %
Rwork0.1972 2832 -
all0.1994 2971 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8118-0.67021.03732.27230.76792.07180.050.1248-0.27020.28620.2683-0.54450.1160.5769-0.31830.1295-0.0111-0.18460.5271-0.24050.691697.00715.624-40.195
22.5958-0.45560.45321.49330.791.6081-0.0374-0.1356-0.01620.36940.1141-0.1495-0.25540.2216-0.07660.0223-0.0661-0.14520.0972-0.06340.169678.133.968-32.155
31.79570.20310.45711.58191.11531.976-0.1062-0.0982-0.16130.2185-0.03660.22440.0484-0.25810.1428-0.07050.0348-0.035-0.0344-0.09650.10252.98925.15-40.103
42.0201-0.2972-0.33692.8830.35361.85450.05040.0944-0.46140.13130.02050.24610.338-0.0058-0.071-0.0357-0.0235-0.05530.0766-0.17710.217856.7240.813-53.255
52.5230.87750.18263.8464-0.28641.71810.0057-0.0097-0.64990.2150.0878-0.69760.4550.4593-0.09350.19390.1041-0.09850.4069-0.30940.710383.849-5.163-52.953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A205 )
2X-RAY DIFFRACTION2(B1 - B205 )
3X-RAY DIFFRACTION3(C1 - C205 )
4X-RAY DIFFRACTION4(D1 - D205 )
5X-RAY DIFFRACTION5(E1 - E205 )

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