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- PDB-5y2q: X-ray structure of acetylcholine binding protein (AChBP) complexe... -

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Basic information

Entry
Database: PDB / ID: 5y2q
TitleX-ray structure of acetylcholine binding protein (AChBP) complexed with a small molecule
ComponentsAcetylcholine-binding protein
KeywordsPROTEIN BINDING/INHIBITOR / Acetylcholine binding protein / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Chem-8L3 / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.363 Å
AuthorsJiang, L.L. / Zhou, L.
CitationJournal: To Be Published
Title: X-ray structure of acetylcholine binding protein (AChBP) complexed with a small molecule
Authors: Jiang, L.L. / Zhou, L.
History
DepositionJul 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 30, 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
D: Acetylcholine-binding protein
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,38010
Polymers120,6245
Non-polymers1,7565
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-51 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.185, 77.156, 222.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSchain AAB2 - 2044 - 206
2GLYGLYchain BBC2 - 2054 - 207
3LYSLYSchain CCD2 - 2044 - 206
4LYSLYSchain DDA2 - 2044 - 206
5LYSLYSchain EEE2 - 2044 - 206

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Components

#1: Protein
Acetylcholine-binding protein / AchBP


Mass: 24124.783 Da / Num. of mol.: 5 / Fragment: UNP residues 21-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Komagataella pastoris (fungus) / References: UniProt: P58154
#2: Chemical
ChemComp-8L3 / 3-[[4-[(3,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]pyridine


Mass: 351.270 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H20Cl2N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: TRIS PH 8.0, AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 47126 / % possible obs: 96.6 % / Redundancy: 7.7 % / Biso Wilson estimate: 50.2 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Χ2: 1.07 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.447.80.8847290.8630.3290.9421.03698.1
2.44-2.547.90.71246500.8930.2660.7621.08897.6
2.54-2.667.80.5246990.9290.1950.5571.08797.2
2.66-2.87.80.36846480.9630.1380.3941.08996.7
2.8-2.977.80.23946620.9840.0890.2561.07496.3
2.97-3.27.80.14646490.9930.0540.1561.0796
3.2-3.537.60.10146380.9960.0380.1081.06495.6
3.53-4.037.30.08246610.9970.0310.0881.02995.2
4.03-5.087.30.05847130.9980.0220.0621.08295.5
5.08-507.70.03950770.9990.0140.0421.07797.6

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHENIXphenix.refine: 1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UX2

1ux2


Resolution: 2.363→45.056 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.94
RfactorNum. reflection% reflection
Rfree0.2768 2325 4.95 %
Rwork0.2233 --
obs0.2258 47013 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.02 Å2 / Biso mean: 37.25 Å2 / Biso min: 11.93 Å2
Refinement stepCycle: final / Resolution: 2.363→45.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 115 144 8252
Biso mean--38.22 32.78 -
Num. residues----999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118304
X-RAY DIFFRACTIONf_angle_d1.44811314
X-RAY DIFFRACTIONf_chiral_restr0.0541280
X-RAY DIFFRACTIONf_plane_restr0.0071449
X-RAY DIFFRACTIONf_dihedral_angle_d12.2023053
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4812X-RAY DIFFRACTION10.428TORSIONAL
12B4812X-RAY DIFFRACTION10.428TORSIONAL
13C4812X-RAY DIFFRACTION10.428TORSIONAL
14D4812X-RAY DIFFRACTION10.428TORSIONAL
15E4812X-RAY DIFFRACTION10.428TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3634-2.41160.41681380.33262469260792
2.4116-2.4640.35671380.3062608274698
2.464-2.52140.39391560.29392599275597
2.5214-2.58440.38421270.28622650277798
2.5844-2.65430.36631460.28922589273597
2.6543-2.73240.33691410.27972607274896
2.7324-2.82060.37191410.26822604274597
2.8206-2.92130.32151410.2652595273696
2.9213-3.03830.30051400.25322614275496
3.0383-3.17650.36611260.24272623274996
3.1765-3.3440.34211370.24452611274896
3.344-3.55340.27571290.23192605273495
3.5534-3.82760.26371440.21982615275995
3.8276-4.21250.25751320.19582613274595
4.2125-4.82150.19871280.17142647277595
4.8215-6.07220.22791390.19192697283696
6.0722-45.06410.23021220.21272942306499

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