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- PDB-5tsf: Crystal structure of AChBP from Aplysia californica complex with ... -

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Basic information

Entry
Database: PDB / ID: 5tsf
TitleCrystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121
ComponentsSoluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN / AChBP / 2-aminopyrimidi9ne complex
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-7KO / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.286 Å
AuthorsCamacho-Hernandez, G.A. / Kaczanowska, K. / Harel, M. / Finn, M.G. / Taylor, P.W.
CitationJournal: To Be Published
Title: Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121
Authors: Camacho-Hernandez, G.A. / Kaczanowska, K. / Harel, M. / Finn, M.G. / Taylor, P.W.
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Oct 4, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,13712
Polymers131,0615
Non-polymers2,0767
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14750 Å2
ΔGint-66 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.190, 115.700, 131.000
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: 26212.105 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): hek923s Gnt1 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-7KO / 6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine


Mass: 326.784 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H15ClN6
#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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4000, 0.1M HEPES pH 7.0, 0.15M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.286→86.72 Å / Num. obs: 61343 / % possible obs: 99.1 % / Redundancy: 13.5 % / Net I/σ(I): 28.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYR.pdb

2byr


Resolution: 2.286→86.72 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2472 3102 5.06 %
Rwork0.1901 --
obs0.193 61262 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.286→86.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 143 414 9046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088930
X-RAY DIFFRACTIONf_angle_d1.08812168
X-RAY DIFFRACTIONf_dihedral_angle_d15.5323290
X-RAY DIFFRACTIONf_chiral_restr0.0721339
X-RAY DIFFRACTIONf_plane_restr0.0051576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.286-2.32170.30881310.21492633X-RAY DIFFRACTION99
2.3217-2.35980.26891090.19332636X-RAY DIFFRACTION100
2.3598-2.40050.25011320.18562593X-RAY DIFFRACTION100
2.4005-2.44410.27441490.18362607X-RAY DIFFRACTION100
2.4441-2.49120.29821280.18752619X-RAY DIFFRACTION100
2.4912-2.5420.26751280.19842628X-RAY DIFFRACTION100
2.542-2.59730.25741290.19932644X-RAY DIFFRACTION100
2.5973-2.65770.24951300.20812620X-RAY DIFFRACTION100
2.6577-2.72420.28551400.21072630X-RAY DIFFRACTION100
2.7242-2.79780.30831610.21022608X-RAY DIFFRACTION100
2.7978-2.88020.30181410.2072618X-RAY DIFFRACTION100
2.8802-2.97310.27391440.212629X-RAY DIFFRACTION100
2.9731-3.07940.24791360.21192618X-RAY DIFFRACTION100
3.0794-3.20270.26951620.19912625X-RAY DIFFRACTION100
3.2027-3.34850.26711300.19882651X-RAY DIFFRACTION100
3.3485-3.5250.24961580.20542626X-RAY DIFFRACTION100
3.525-3.74590.32241560.2352634X-RAY DIFFRACTION100
3.7459-4.03510.23361680.18952621X-RAY DIFFRACTION100
4.0351-4.44110.18271420.14752674X-RAY DIFFRACTION100
4.4411-5.08370.17731390.13932691X-RAY DIFFRACTION100
5.0837-6.40470.19831380.17092733X-RAY DIFFRACTION100
6.4047-86.78190.19611510.17852822X-RAY DIFFRACTION99

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