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- PDB-3zdh: Crystal structure of Ls-AChBP complexed with carbamoylcholine ana... -

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Basic information

Entry
Database: PDB / ID: 3zdh
TitleCrystal structure of Ls-AChBP complexed with carbamoylcholine analogue N,N-dimethyl-4-(1-methyl-1H-imidazol-2-yloxy)butan-2-amine
ComponentsACETYLCHOLINE BINDING PROTEIN
KeywordsACETYLCHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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-XRS / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å
AuthorsUssing, C.A. / Hansen, C.P. / Petersen, J.G. / Jensen, A.A. / Rohde, L.A.H. / Ahring, P.K. / Nielsen, E.O. / Kastrup, J.S. / Gajhede, M. / Frolund, B. / Balle, T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Synthesis, Pharmacology, and Biostructural Characterization of Novel Alpha(4)Beta(2) Nicotinic Acetylcholine Receptor Agonists.
Authors: Ussing, C.A. / Hansen, C.P. / Petersen, J.G. / Jensen, A.A. / Rohde, L.A.H. / Ahring, P.K. / Nielsen, E.O. / Kastrup, J.S. / Gajhede, M. / Frolund, B. / Balle, T.
History
DepositionNov 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)241,23324
Polymers238,62510
Non-polymers2,60714
Water18,1771009
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)120,71213
Polymers119,3135
Non-polymers1,4008
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-65.3 kcal/mol
Surface area41150 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)120,52011
Polymers119,3135
Non-polymers1,2086
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-42.3 kcal/mol
Surface area41270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.334, 143.822, 115.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
211CHAIN B AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
311CHAIN C AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
411CHAIN D AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
511CHAIN E AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
611CHAIN F AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
711CHAIN G AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
811CHAIN H AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
911CHAIN I AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...
1011CHAIN J AND (RESSEQ 1:39 OR RESSEQ 48:155 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.332179, 0.92139, -0.201737), (-0.942145, 0.334317, -0.02441), (0.044953, 0.198174, 0.979135)
Vector: 41.6481, 21.5204, 2.13901)

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Components

#1: Protein
ACETYLCHOLINE BINDING PROTEIN / ACH-BINDING PROTEIN / ACHBP


Mass: 23862.523 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYMNAEA STAGNALIS (great pond snail) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P58154
#2: Chemical
ChemComp-XRS / (2R)-N,N-dimethyl-4-(1-methylimidazol-2-yl)oxy-butan-2-amine


Mass: 197.277 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H19N3O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE UNIPROT SEQUENCE INCLUDES THE SIGNAL PEPTIDE

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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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.5
Details: 0.1 M TRIS (PH 8.5), 2.0 M AMMONIUM SULPHATE, 2 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2010 / Details: DOUBLE MIRRORS
RadiationMonochromator: DOUBLE SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.19→19.68 Å / Num. obs: 115372 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.2
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZDG

3zdg


Resolution: 2.195→19.684 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: MLHL / Details: RESIDUES 156-162 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2449 2004 1.7 %
Rwork0.1912 --
obs0.1921 115174 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.195→19.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16028 0 178 1009 17215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816743
X-RAY DIFFRACTIONf_angle_d1.10322832
X-RAY DIFFRACTIONf_dihedral_angle_d12.9686263
X-RAY DIFFRACTIONf_chiral_restr0.0692599
X-RAY DIFFRACTIONf_plane_restr0.0052935
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1486X-RAY DIFFRACTIONPOSITIONAL
12B1486X-RAY DIFFRACTIONPOSITIONAL0.063
13C1496X-RAY DIFFRACTIONPOSITIONAL0.058
14D1512X-RAY DIFFRACTIONPOSITIONAL0.05
15E1496X-RAY DIFFRACTIONPOSITIONAL0.064
16F1495X-RAY DIFFRACTIONPOSITIONAL0.048
17G1480X-RAY DIFFRACTIONPOSITIONAL0.062
18H1505X-RAY DIFFRACTIONPOSITIONAL0.056
19I1488X-RAY DIFFRACTIONPOSITIONAL0.05
110J1499X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1947-2.2730.33841860.263310333X-RAY DIFFRACTION91
2.273-2.36380.30951940.237411303X-RAY DIFFRACTION99
2.3638-2.47120.2882040.228111268X-RAY DIFFRACTION100
2.4712-2.60130.28882060.214611314X-RAY DIFFRACTION100
2.6013-2.76380.26661970.205411374X-RAY DIFFRACTION100
2.7638-2.97650.26832060.208311369X-RAY DIFFRACTION100
2.9765-3.27490.25961960.197311417X-RAY DIFFRACTION100
3.2749-3.74590.23982010.180511417X-RAY DIFFRACTION100
3.7459-4.70870.19822080.153511552X-RAY DIFFRACTION100
4.7087-19.68450.20612060.174511823X-RAY DIFFRACTION99

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