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- PDB-5j5h: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 5j5h
TitleX-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH 6-(2-methoxyphenyl)-N4,N4-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / 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-6GK / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKaczanowska, K. / Harel, M. / Camacho Hernandez, A.G. / Taylor, P.
Funding support United States, 1items
OrganizationGrant numberCountry
University of California 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

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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)255,83641
Polymers248,59510
Non-polymers7,24131
Water2,522140
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 area19090 Å2
ΔGint-97 kcal/mol
Surface area41350 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)127,96621
Polymers124,2975
Non-polymers3,66816
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19550 Å2
ΔGint-107 kcal/mol
Surface area41400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.726, 130.443, 107.689
Angle α, β, γ (deg.)90.000, 103.320, 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-6GK / 6-(2-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
#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.: 11 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
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: Jul 2, 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
ReflectionLimit h max: 44 / Limit h min: -46 / Limit k max: 56 / Limit k min: 0 / Limit l max: 46 / Limit l min: 0 / Number: 120631 / D res high: 2.326 Å / D res low: 104.83 Å / Num. obs: 118832
ReflectionResolution: 2.32→50 Å / Num. obs: 119964 / % possible obs: 96.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 58.75 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.049 / Rrim(I) all: 0.113 / Χ2: 1.311 / Net I/av σ(I): 18.762 / Net I/σ(I): 6.7 / Num. measured all: 867005
Reflection scaleGroup code: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.32-2.36546840.3450.8410.64676.3
2.36-2.45.553710.370.670.64587
2.4-2.45659230.4380.6060.64195
2.45-2.56.860800.5410.5380.64698.9
2.5-2.557.462070.6280.4810.65599.9
2.55-2.617.661340.7230.4070.671100
2.61-2.687.762020.8730.2770.8121000.720.771
2.68-2.757.761890.8730.2890.7051000.750.804
2.75-2.837.761560.8920.2120.7021000.5510.591
2.83-2.927.761690.930.1630.7331000.4230.454
2.92-3.037.762030.9660.1150.7581000.2990.321
3.03-3.157.761750.9790.0880.7961000.2290.245
3.15-3.297.761810.990.0630.8461000.1630.174
3.29-3.477.762170.9920.0551.311000.1420.152
3.47-3.686.860100.9460.0965.10396.70.2270.247
3.68-3.976.850350.9870.0542.40981.10.130.141
3.97-4.377.661990.9970.0272.0941000.070.076
4.37-57.662280.9950.0293.4691000.0740.08
5-6.297.562670.9980.0211.7661000.0540.058
6.29-507.6633410.0090.78299.90.0240.026

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.47 Å48.64 Å
Translation7.47 Å48.64 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
PHENIX2.5.5model building
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.635 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2969 1299 1.67 %
Rwork0.2221 76282 -
obs0.2233 77581 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.88 Å2 / Biso mean: 55.4833 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.7→48.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16598 0 495 140 17233
Biso mean--62.02 46.46 -
Num. residues----2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117553
X-RAY DIFFRACTIONf_angle_d1.32423923
X-RAY DIFFRACTIONf_chiral_restr0.052689
X-RAY DIFFRACTIONf_plane_restr0.0063082
X-RAY DIFFRACTIONf_dihedral_angle_d16.1916511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80810.36841480.270686298777100
2.8081-2.93590.35581450.247186258770100
2.9359-3.09060.27661490.22786898838100
3.0906-3.28420.34011470.233986598806100
3.2842-3.53770.33981470.25478558870599
3.5377-3.89360.4581290.29797933806291
3.8936-4.45670.30081320.18367704783688
4.4567-5.61370.23121490.175487008849100
5.6137-48.64320.21441530.207187858938100

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