PDB-7pdr: Crystal structure of Lymnaea stagnalis Acetylcholine-binding prot...

ID or keywords:

Entry

Database: PDB / ID: 7pdr

Title

Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP) Q55R/M114V double mutant complexed with Dichloromezotiaz

Components

Acetylcholine-binding protein

Keywords

SIGNALING PROTEIN /

Acetylcholine /

protein /

insecticide

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity /

synaptic cleft / transmembrane signaling receptor activity /

synapse /

membrane
Similarity search - Function

Biological species

Lymnaea stagnalis (great pond snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Montgomery, M.G.

Funding support

United Kingdom, 1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators.
Authors: Montgomery, M. / Rendine, S. / Zimmer, C.T. / Elias, J. / Schaetzer, J. / Pitterna, T. / Benfatti, F. / Skaljac, M. / Bigot, A.

History

Deposition	Aug 6, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7pdr.cif.gz	209.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7pdr.ent.gz		Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/7pdr ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pdr	HTTPS FTP

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Related structure data

Related structure data	7pd6C 7pdbC 7pe5C 7pe6C 1uv6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7pe5-d 5y2q-d 5bp0-1 7pe6-d 7pd6-2 5bp0-2 7n0y-d 3u8m-3 3u8n-3 4zru-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#71 - Nov 2005 Acetylcholine Receptor similarity (5) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4)

Deposited unit

AaA: Acetylcholine-binding protein

BaB: Acetylcholine-binding protein

CaC: Acetylcholine-binding protein

DaD: Acetylcholine-binding protein

EaE: Acetylcholine-binding protein

hetero molecules

121 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.040, 74.040, 350.930
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	2	Chains AAA CCC
3	3	Chains AAA DDD
4	4	Chains AAA EEE
5	5	Chains BBB CCC
6	6	Chains BBB DDD
7	7	Chains BBB EEE
8	8	Chains CCC DDD
9	9	Chains CCC EEE
10	10	Chains DDD EEE

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Acetylcholine-binding protein / ACh-binding protein / AchBP Mass: 23818.428 Da / Num. of mol.: 5 / Mutation: Q55R, N66D, M114V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Komagataella pastoris (fungus) / References: UniProt: P58154
#2: Chemical	ChemComp-7JI / 3-[3,5-bis(chloranyl)phenyl]-1-[(2-chloranyl-1,3-thiazol-5-yl)methyl]-9-methyl-pyrido[1,2-a]pyrimidine-2,4-dione Mass: 452.741 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₉H₁₂Cl₃N₃O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 14-18% PEG3350, 0.1-0.25M diammonium hydrogen citrate, 15% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.33→60.23 Å / Num. obs: 46264 / % possible obs: 100 % / Redundancy: 10.2 % / B_iso Wilson estimate: 51.57 Å² / R_merge(I) obs: 0.068 / R_pim(I) all: 0.024 / R_rim(I) all: 0.076 / Net I/σ(I): 21
Reflection shell	Resolution: 2.33→2.39 Å / Redundancy: 10.1 % / R_merge(I) obs: 0.967 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3469 / R_pim(I) all: 0.335 / R_rim(I) all: 1.07 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UV6

1uv6

Resolution: 2.33→60.225 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.94 / WR_factor R_free: 0.237 / WR_factor R_work: 0.207 / Average fsc free: 0.8559 / Average fsc work: 0.8651 / Cross valid method: FREE R-VALUE / ESU R: 0.431 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2449	2310	5.001 %
R_work	0.2171	43878	-
all	0.219	-	-
obs	-	46188	99.957 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 37.559 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.792 Å²	0.896 Å²	0 Å²
2-	-	1.792 Å²	-0 Å²
3-	-	-	-5.815 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→60.225 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7905	0	140	34	8079

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	8256
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	7391
X-RAY DIFFRACTION	r_angle_refined_deg	1.738	1.641	11289
X-RAY DIFFRACTION	r_angle_other_deg	2.381	1.574	17135
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.338	5	982
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.053	21.589	453
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.748	15	1327
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.111	15	69
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1100
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9193
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	1776
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	1168
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	6614
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	3982
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	3810
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.101	0.2	140
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.324	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.301	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.261	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.815	3.737	3952
X-RAY DIFFRACTION	r_mcbond_other	2.812	3.737	3950
X-RAY DIFFRACTION	r_mcangle_it	4.383	5.589	4920
X-RAY DIFFRACTION	r_mcangle_other	4.381	5.589	4920
X-RAY DIFFRACTION	r_scbond_it	3.898	4.244	4304
X-RAY DIFFRACTION	r_scbond_other	3.897	4.243	4305
X-RAY DIFFRACTION	r_scangle_it	6.161	6.171	6367
X-RAY DIFFRACTION	r_scangle_other	6.161	6.171	6368
X-RAY DIFFRACTION	r_lrange_it	8.291	41.61	8537
X-RAY DIFFRACTION	r_lrange_other	8.291	41.608	8536
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.087	0.05	5890
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	5935
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.099	0.05	5909
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.088	0.05	5942
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.086	0.05	5969
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.099	0.05	5902
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.086	0.05	6047
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.099	0.05	5941
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.08	0.05	6052
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.097	0.05	5959

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.33-2.39	0.345	153	0.333	3310	0.333	3467	0.681	0.704	99.8846	0.303
2.39-2.456	0.348	169	0.315	3110	0.316	3280	0.751	0.768	99.9695	0.279
2.456-2.527	0.321	161	0.3	3059	0.301	3220	0.793	0.812	100	0.265
2.527-2.605	0.331	154	0.299	2969	0.3	3125	0.784	0.808	99.936	0.263
2.605-2.69	0.35	121	0.273	2910	0.276	3034	0.825	0.841	99.9011	0.236
2.69-2.784	0.294	132	0.273	2834	0.274	2967	0.857	0.857	99.9663	0.237
2.784-2.889	0.33	153	0.275	2679	0.278	2833	0.823	0.847	99.9647	0.243
2.889-3.007	0.312	119	0.255	2610	0.257	2731	0.849	0.87	99.9268	0.226
3.007-3.14	0.285	151	0.256	2488	0.258	2639	0.874	0.883	100	0.233
3.14-3.293	0.251	143	0.241	2364	0.242	2507	0.898	0.895	100	0.226
3.293-3.47	0.268	131	0.233	2253	0.235	2384	0.898	0.916	100	0.224
3.47-3.68	0.227	111	0.232	2158	0.232	2269	0.927	0.924	100	0.226
3.68-3.933	0.281	109	0.219	2005	0.222	2114	0.9	0.921	100	0.215
3.933-4.247	0.195	122	0.193	1851	0.193	1974	0.954	0.949	99.9493	0.196
4.247-4.65	0.194	82	0.165	1747	0.166	1829	0.947	0.957	100	0.173
4.65-5.195	0.209	81	0.159	1553	0.161	1634	0.952	0.963	100	0.166
5.195-5.991	0.191	71	0.159	1383	0.16	1454	0.965	0.962	100	0.166
5.991-7.319	0.224	67	0.18	1175	0.183	1242	0.937	0.947	100	0.188
7.319-10.275	0.149	56	0.148	906	0.148	962	0.968	0.969	100	0.164
10.275-60.225	0.301	24	0.247	514	0.249	541	0.923	0.932	99.4455	0.26

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