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- PDB-4qaa: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 4qaa
TitleX-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH 6-(4-Methoxyphenyl)-N4-octylpyrimidine-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-KK1 / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKaczanowska, K. / Harel, M. / Radic, Z. / Changeux, J.-P. / Finn, M.G. / Taylor, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for cooperative interactions of substituted 2-aminopyrimidines with the acetylcholine binding protein.
Authors: Kaczanowska, K. / Harel, M. / Radic, Z. / Changeux, J.P. / Finn, M.G. / Taylor, P.
History
DepositionMay 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)254,76449
Polymers247,46310
Non-polymers7,30139
Water2,900161
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)127,62027
Polymers123,7325
Non-polymers3,88822
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-115 kcal/mol
Surface area42970 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)127,14522
Polymers123,7325
Non-polymers3,41317
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18600 Å2
ΔGint-103 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.414, 129.934, 122.752
Angle α, β, γ (deg.)90.00, 106.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 24746.338 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-KK1 / 6-(4-methoxyphenyl)-N~4~-octylpyrimidine-2,4-diamine


Mass: 328.452 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C19H28N4O
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.26 M ammonium phosphate monobasic, 35% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2013
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.65 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 3486 5.06 %
Rwork0.193 --
obs0.197 68911 99.8 %
all-68911 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16675 0 451 161 17287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817515
X-RAY DIFFRACTIONf_angle_d1.21623827
X-RAY DIFFRACTIONf_dihedral_angle_d17.8226496
X-RAY DIFFRACTIONf_chiral_restr0.082672
X-RAY DIFFRACTIONf_plane_restr0.0053041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7370.34261390.24382579X-RAY DIFFRACTION100
2.737-2.77610.33981470.24852649X-RAY DIFFRACTION100
2.7761-2.81750.32441480.24332560X-RAY DIFFRACTION100
2.8175-2.86150.30341340.22552624X-RAY DIFFRACTION100
2.8615-2.90840.33261320.22842588X-RAY DIFFRACTION100
2.9084-2.95860.32621290.23122620X-RAY DIFFRACTION100
2.9586-3.01240.32421380.21782594X-RAY DIFFRACTION100
3.0124-3.07030.31121350.20322629X-RAY DIFFRACTION100
3.0703-3.1330.30411320.21672602X-RAY DIFFRACTION100
3.133-3.20110.32821320.21592635X-RAY DIFFRACTION100
3.2011-3.27550.321620.21382569X-RAY DIFFRACTION100
3.2755-3.35740.27341350.20892630X-RAY DIFFRACTION100
3.3574-3.44820.31731360.19932606X-RAY DIFFRACTION100
3.4482-3.54960.26541290.19082607X-RAY DIFFRACTION100
3.5496-3.66420.22771340.18152635X-RAY DIFFRACTION100
3.6642-3.79510.26881510.18962631X-RAY DIFFRACTION100
3.7951-3.9470.24421310.18442608X-RAY DIFFRACTION100
3.947-4.12650.3011460.18672609X-RAY DIFFRACTION100
4.1265-4.3440.24211570.17482614X-RAY DIFFRACTION100
4.344-4.61590.25211390.17232627X-RAY DIFFRACTION100
4.6159-4.9720.20671570.16162607X-RAY DIFFRACTION100
4.972-5.47180.23441360.17562623X-RAY DIFFRACTION100
5.4718-6.26230.22671390.18352633X-RAY DIFFRACTION100
6.2623-7.88470.24341420.19112658X-RAY DIFFRACTION100
7.8847-49.66040.20011260.19712688X-RAY DIFFRACTION99

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