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- PDB-3peo: Crystal structure of acetylcholine binding protein complexed with... -

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Basic information

Entry
Database: PDB / ID: 3peo
TitleCrystal structure of acetylcholine binding protein complexed with metocurine
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / Receptor / Curarines binding / acetylcholine binding protein / CHOLINE BINDING PROTEIN
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-CU9 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTalley, T.T. / Harel, M. / Yamauchi, G.J. / Radic, Z. / Hansen, S. / Huxford, T. / Taylor, P.W.
CitationJournal: To be Published
Title: The curare alkaloids: analyzing the poses of complexes with the acetylcholine binding protein in relation to structure and binding energetics
Authors: Talley, T.T. / Harel, M. / Yamauchi, G.J. / Radic, Z. / Hansen, S. / Huxford, T. / Taylor, P.W.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / struct_keywords ...entity_src_gen / struct_keywords / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
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)264,90118
Polymers259,67810
Non-polymers5,2238
Water23,6001310
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)132,4509
Polymers129,8395
Non-polymers2,6114
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint-59 kcal/mol
Surface area43470 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)132,4509
Polymers129,8395
Non-polymers2,6114
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-59 kcal/mol
Surface area43370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.699, 147.574, 148.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 25967.832 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-CU9 / 6,6',7',12'-tetramethoxy-2,2,2',2'-tetramethyltubocuraran-2,2'-diium / metocurine / Metocurine


Mass: 652.819 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H48N2O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1310 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 4000, 0.25M magnesium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→104.828 Å / Num. all: 160070 / Num. obs: 158959 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.119 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1-2.26199.2
2.26-2.49199.6
2.49-2.85199.9
2.85-3.59199.9
3.59-104.828199.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn


Resolution: 2.1→104.828 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.679 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25496 1593 1 %RANDOM
Rwork0.20776 ---
obs0.20825 157366 99.31 %-
all-159376 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→104.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16443 0 384 1310 18137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02217384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.97823792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04852075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13424.353811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.656152761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.25415102
X-RAY DIFFRACTIONr_chiral_restr0.1480.22623
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02113298
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.27396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.211791
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3361.510370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.354216957
X-RAY DIFFRACTIONr_scbond_it3.47137014
X-RAY DIFFRACTIONr_scangle_it5.2584.56819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 99 -
Rwork0.258 11419 -
obs--98.45 %

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