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- PDB-6qkk: Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyri... -

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Basic information

Entry
Database: PDB / ID: 6qkk
TitleAplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (1)
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / AChBP / Acetylcholine
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-H92 / OXALATE ION / PHOSPHATE ION / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavis, S. / Bueno, R.V. / Dawson, A. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Interactions between 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors
Authors: Bueno, R.V. / Davis, S. / Dawson, A. / Ondachi, P.W. / Carroll, F.I. / Hunter, W.N.
History
DepositionJan 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 2, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,78675
Polymers283,26810
Non-polymers7,51965
Water20,5011138
1
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)145,43738
Polymers141,6345
Non-polymers3,80333
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-8 kcal/mol
Surface area40510 Å2
MethodPISA
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,34937
Polymers141,6345
Non-polymers3,71532
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21600 Å2
ΔGint-8 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.995, 131.583, 131.825
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 14 molecules ABCDEFGHIJ

#1: Protein
Soluble acetylcholine receptor


Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: all disulfide bonds have been represented as oxidised, as due to radiation damage the exact oxidation state of the disulfides in some chains is unclear. The sequence conflicts are because we ...Details: all disulfide bonds have been represented as oxidised, as due to radiation damage the exact oxidation state of the disulfides in some chains is unclear. The sequence conflicts are because we have used the AChBP gene sequence provided in the Aplysia californica genome (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=589127391_t0Vv5jEv8KyWGt7MjPEaZKNxTL3u&redirect=manual&source=genome.cse.ucsc.edu), which differs from the UniProt Q8WSF8 Sequence by identifying both ALA 60 and and ALA 155 as VAL
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1199 molecules

#2: Chemical
ChemComp-H92 / 4-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]benzamide


Mass: 311.353 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H18FN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsall disulfide bonds have been represented as oxidised, as due to radiation damage the exact ...all disulfide bonds have been represented as oxidised, as due to radiation damage the exact oxidation state of the disulfides in some chains is unclear

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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: 3.39 Å3/Da / Density % sol: 63.68 % / Description: Block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Reservoir: 0.2 M NaCl, 0.1 M Phosphate/citrate pH 4.2 12% PEG 8000 Buffer: 50 mM Tris, 250 mM NaCl pH 7.5 Protein concentration 4 mg/ml Microseeded

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.2→48.88 Å / Num. obs: 177603 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.172 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2 / Num. unique obs: 8766 / CC1/2: 0.43 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XYS

2xys


Resolution: 2.2→48.88 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.562 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22828 8867 5 %RANDOM
Rwork0.19872 ---
obs0.2002 168732 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.569 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å2-0.61 Å2
2--2.37 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16442 0 502 1138 18082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01517366
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715008
X-RAY DIFFRACTIONr_angle_refined_deg0.971.76623656
X-RAY DIFFRACTIONr_angle_other_deg0.3541.73635243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.3165.3272111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.63419.82611
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72152340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5761594
X-RAY DIFFRACTIONr_chiral_restr0.0450.22293
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02221788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.8478225
X-RAY DIFFRACTIONr_mcbond_other0.9761.8488226
X-RAY DIFFRACTIONr_mcangle_it1.7832.76210272
X-RAY DIFFRACTIONr_mcangle_other1.7842.76310272
X-RAY DIFFRACTIONr_scbond_it0.9791.9999139
X-RAY DIFFRACTIONr_scbond_other0.97929140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7432.93913384
X-RAY DIFFRACTIONr_long_range_B_refined3.8422.1617862
X-RAY DIFFRACTIONr_long_range_B_other3.76222.04217688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 681 -
Rwork0.283 12384 -
obs--99.95 %

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