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- PDB-2y54: Fragment growing induces conformational changes in acetylcholine-... -

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Basic information

Entry
Database: PDB / ID: 2y54
TitleFragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Fragment 1)
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR
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
[(1R,5S)-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)125,00418
Polymers123,4435
Non-polymers1,56113
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-125.1 kcal/mol
Surface area44830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.420, 216.420, 216.420
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-V63 / [(1R,5S)-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE


Mass: 231.290 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H17NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
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: 3.64 Å3/Da / Density % sol: 66.22 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M MMT PH7.5, 0.9M 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: 3.65→16.33 Å / Num. obs: 18887 / % possible obs: 100 % / Observed criterion σ(I): 2.78 / Redundancy: 5 % / Biso Wilson estimate: 55.02 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.19
Reflection shellResolution: 3.65→3.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.78 / % possible all: 100

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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: 3.65→48.39 Å / Cor.coef. Fo:Fc: 0.8877 / Cor.coef. Fo:Fc free: 0.8573 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 974 5.16 %RANDOM
Rwork0.1922 ---
obs0.1935 18858 --
Displacement parametersBiso mean: 75.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.705 Å
Refinement stepCycle: LAST / Resolution: 3.65→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 101 0 8281
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088493HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9411597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes225HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1200HARMONIC5
X-RAY DIFFRACTIONt_it8493HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion3.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1130SEMIHARMONIC5
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_contact8404SEMIHARMONIC4
LS refinement shellResolution: 3.65→3.87 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2399 144 4.73 %
Rwork0.212 2898 -
all0.2133 3042 -
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)
12.185-0.40270.49642.81970.63562.66370.04420.1684-0.04880.24380.2072-0.50790.02020.4557-0.2514-0.0580.0053-0.17820.3201-0.09780.56895.90715.455-39.33
22.5699-0.08370.15272.14090.5322.7056-0.1053-0.15340.14120.43250.1879-0.1659-0.42580.0766-0.08260.05250.0128-0.14440.0516-0.07750.257876.99433.698-31.357
32.20880.03940.38652.25010.11783.552-0.081-0.1927-0.03370.1913-0.01760.1951-0.0084-0.40980.09860.00020.0471-0.0150.1768-0.06150.209752.10424.682-39.18
41.1894-0.1431-0.25832.0950.27272.25750.10780.0768-0.37370.11180.03160.19080.1286-0.0953-0.13940.0298-0.0605-0.04880.2184-0.06110.376356.0330.506-52.269
51.40650.1309-0.25483.6926-0.81722.378-0.07210.1285-0.4582-0.11340.1411-0.66440.4640.3755-0.06890.03380.0271-0.09150.362-0.16070.627183.024-5.251-52.087
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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