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- PDB-5brx: X-ray crystal structure of Aplysia californica (Ac-AChBP) in comp... -

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Basic information

Entry
Database: PDB / ID: 5brx
TitleX-ray crystal structure of Aplysia californica (Ac-AChBP) in complex with 2-pyridyl azatricyclo[3.3.1.13,7]decane; 2-pyridylazaadamantane; 2-Aza (TI-8480)
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / nicotine / acetylcholine
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
Chem-TI4 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
CitationJournal: To Be Published
Title: Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs
Authors: Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 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
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)265,33530
Polymers262,35110
Non-polymers2,98320
Water9,458525
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)132,66715
Polymers131,1765
Non-polymers1,49210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-61 kcal/mol
Surface area44010 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)132,66715
Polymers131,1765
Non-polymers1,49210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-61 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.297, 98.297, 270.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 26235.141 Da / Num. of mol.: 10 / Fragment: UNP residues 18-236 / Mutation: Y55W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK GNT1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TI4 / (2R,3S,5R,7S)-2-(pyridin-3-yl)-1-azatricyclo[3.3.1.1~3,7~]decane


Mass: 214.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H18N2
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 159523 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.156 / Χ2: 1.072 / Net I/av σ(I): 17.273 / Net I/σ(I): 5.5 / Num. measured all: 2019957
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
2.05-2.098.60.879391.007
2.09-2.12110.83279350.656
2.12-2.1612.10.74979430.668
2.16-2.2112.50.66879580.696
2.21-2.2612.80.63979540.886
2.26-2.3112.90.58279730.745
2.31-2.3712.90.4779990.724
2.37-2.4312.90.42279490.696
2.43-2.512.90.39879780.731
2.5-2.5812.80.35380240.748
2.58-2.6812.80.29779360.743
2.68-2.7812.70.24279720.744
2.78-2.9112.70.19679490.777
2.91-3.0612.80.1579700.829
3.06-3.2512.80.11679710.974
3.25-3.5112.80.09480051.264
3.51-3.86130.08579871.608
3.86-4.4213.40.07579702.294
4.42-5.5613.80.06380322.104
5.56-5015.10.04980792.055

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of 2byn, 2byr, 2bys, and 2pgz

2byn

2byr

2bys

2pgz


Resolution: 2.05→49.149 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2001 1.26 %
Rwork0.1971 157317 -
obs0.1975 159318 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.88 Å2 / Biso mean: 22.2867 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 2.05→49.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16340 0 376 525 17241
Biso mean--34.84 21.48 -
Num. residues----2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716947
X-RAY DIFFRACTIONf_angle_d1.17223147
X-RAY DIFFRACTIONf_chiral_restr0.0412627
X-RAY DIFFRACTIONf_plane_restr0.0042972
X-RAY DIFFRACTIONf_dihedral_angle_d12.4445888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0504-2.10170.27721420.22691116611308
2.1017-2.15850.3121450.22381120611351
2.1585-2.22210.26261390.22061120011339
2.2221-2.29380.27531430.21611124111384
2.2938-2.37580.26261430.20751123511378
2.3758-2.47090.26811470.21421126411411
2.4709-2.58330.23771430.22091124911392
2.5833-2.71950.31591470.21811117611323
2.7195-2.88990.29171420.21841127611418
2.8899-3.1130.27511460.22361119211338
3.113-3.42620.26621460.20581125611402
3.4262-3.92180.17991360.18241129311429
3.9218-4.94030.16411430.1511126511408
4.9403-49.16260.17661390.17241129811437

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