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- PDB-5j5g: X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) ... -

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Basic information

Entry
Database: PDB / ID: 5j5g
TitleX-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with 6-(4-methoxyphenyl)-N4,N4-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / 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-6GF / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.036 Å
AuthorsKaczanowska, K. / Harel, M. / Camacho Hernandez, A.G. / Taylor, P.
Funding support United States, 1items
OrganizationGrant numberCountry
University of CaliforniaTRDRP 21FT-0024 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Substituted 2-Aminopyrimidines Selective for alpha 7-Nicotinic Acetylcholine Receptor Activation and Association with Acetylcholine Binding Proteins.
Authors: Kaczanowska, K. / Camacho Hernandez, G.A. / Bendiks, L. / Kohs, L. / Cornejo-Bravo, J.M. / Harel, M. / Finn, M.G. / Taylor, P.
History
DepositionApr 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,74140
Polymers248,59510
Non-polymers7,14630
Water23,8161322
1
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,87120
Polymers124,2975
Non-polymers3,57315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-96 kcal/mol
Surface area42550 Å2
MethodPISA
2
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,87120
Polymers124,2975
Non-polymers3,57315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19660 Å2
ΔGint-98 kcal/mol
Surface area42650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.720, 125.748, 118.728
Angle α, β, γ (deg.)90.000, 109.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetylcholine-binding protein / AchBP


Mass: 24859.496 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pFLAG-CMV3 / Cell line (production host): Hek293s Gnt1 / Production host: Homo sapiens (human) / References: UniProt: P58154
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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
#4: Chemical
ChemComp-6GF / 6-(4-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine


Mass: 398.460 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C23H22N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.26 M ammonium phosphate monobasic, 35% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2015 / Details: 3 x 3 CCD array
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 154549 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Rrim(I) all: 0.134 / Χ2: 1.068 / Net I/av σ(I): 21.667 / Net I/σ(I): 6.7 / Num. measured all: 1146080
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.086.10.58872360.8870.2520.6420.71294.2
2.08-2.116.80.56177470.9170.2310.6070.728100
2.11-2.156.90.49676890.9360.2020.5360.739100
2.15-2.27.10.46377530.9430.1860.4990.753100
2.2-2.257.30.43477470.9550.1720.4680.784100
2.25-2.37.50.40377270.9640.1580.4330.796100
2.3-2.357.60.36276780.9710.1410.3880.793100
2.35-2.427.60.33177390.9750.1280.3550.821100
2.42-2.497.70.29777360.980.1150.3190.835100
2.49-2.577.70.27777340.9820.1070.2970.845100
2.57-2.667.70.23777540.9860.0920.2550.868100
2.66-2.777.70.20177160.9890.0780.2160.895100
2.77-2.897.70.17177790.9920.0660.1830.937100
2.89-3.057.70.13577100.9950.0520.1450.998100
3.05-3.247.70.11177670.9960.0430.1191.07100
3.24-3.497.60.08877800.9960.0340.0941.28100
3.49-3.847.60.0877840.9960.0310.0861.771100
3.84-4.397.50.07277690.9960.0280.0772.23399.9
4.39-5.547.40.05877810.9980.0230.0621.785100
5.54-507.60.04979230.9990.0190.0531.519100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.22 Å49.54 Å
Translation7.22 Å49.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data collection
HKL-2000data reduction
PHENIX2.5.5model building
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QAC

4qac


Resolution: 2.036→49.54 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1996 1.29 %
Rwork0.1663 152493 -
obs0.1669 154489 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.28 Å2 / Biso mean: 27.7174 Å2 / Biso min: 9.54 Å2
Refinement stepCycle: final / Resolution: 2.036→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17224 0 490 1322 19036
Biso mean--35.07 30.77 -
Num. residues----2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818365
X-RAY DIFFRACTIONf_angle_d1.13725083
X-RAY DIFFRACTIONf_chiral_restr0.0462811
X-RAY DIFFRACTIONf_plane_restr0.0053259
X-RAY DIFFRACTIONf_dihedral_angle_d14.4076882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0364-2.08730.23911330.196102121034594
2.0873-2.14370.23171460.17811088511031100
2.1437-2.20680.22221470.16961087611023100
2.2068-2.27810.20331310.16711095911090100
2.2781-2.35950.20811470.16971089211039100
2.3595-2.45390.24981510.1711090711058100
2.4539-2.56560.27351320.17751092511057100
2.5656-2.70090.22581450.17561094311088100
2.7009-2.87010.23631440.17731090811052100
2.8701-3.09160.20331420.16951094811090100
3.0916-3.40270.23271400.1711099911139100
3.4027-3.89490.19851480.15411092211070100
3.8949-4.90650.16251450.14181101311158100
4.9065-49.55410.19341450.17431110411249100

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