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- PDB-3wti: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 3wti
TitleCrystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Clothianidin
ComponentsAcetylcholine-binding protein
KeywordsSIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / clothianidin / acetylcholine binding
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-CT4 / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsOkajima, T. / Ihara, M. / Yamashita, A. / Oda, T. / Matsuda, K.
CitationJournal: Mol.Pharmacol. / Year: 2014
Title: Studies on an acetylcholine binding protein identify a basic residue in loop G on the beta 1 strand as a new structural determinant of neonicotinoid actions
Authors: Ihara, M. / Okajima, T. / Yamashita, A. / Oda, T. / Asano, T. / Matsui, M. / Sattelle, D.B. / Matsuda, K.
History
DepositionApr 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,50310
Polymers121,2545
Non-polymers1,2485
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-44 kcal/mol
Surface area43230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.145, 74.145, 351.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 24250.875 Da / Num. of mol.: 5 / Fragment: UNP residues 21-229 / Mutation: Q55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P58154
#2: Chemical
ChemComp-CT4 / 1-[(2-chloro-1,3-thiazol-5-yl)methyl]-3-methyl-2-nitroguanidine


Mass: 249.678 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8ClN5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N- ...AUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N-GLYCOSIDASE F. THE CONFLICT IS DUE TO POST-TRANSLATIONAL MODIFICATION AND SAMPLE PREPARATION.

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.7
Details: 0.2M Na citrate pH 5.7, 15-22% PEG3350, 0.5mM clothianidin, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.67→39.6 Å / Num. all: 30602 / Num. obs: 30565 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→39.6 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 44.925 / SU ML: 0.412 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29395 1519 5 %RANDOM
Rwork0.22464 ---
obs0.22814 28941 99.58 %-
all-30462 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.68→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 75 178 8532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198589
X-RAY DIFFRACTIONr_bond_other_d00.027871
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.93911716
X-RAY DIFFRACTIONr_angle_other_deg3.634318127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7851043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65523.63416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.863151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0831580
X-RAY DIFFRACTIONr_chiral_restr0.060.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021973
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it024162
X-RAY DIFFRACTIONr_mcbond_other024159
X-RAY DIFFRACTIONr_mcangle_it035190
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it02.0064427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.678→2.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 103 -
Rwork0.339 2150 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47270.095-1.29891.3468-0.46994.8457-0.00680.0606-0.3662-0.0614-0.053-0.05650.68150.210.05990.1390.0721-0.0410.0987-0.01740.115646.6527-20.0819-25.1767
21.835-0.35560.03821.26140.03013.82180.01170.0243-0.1747-0.06160.11280.19170.4926-0.5388-0.12450.1359-0.1301-0.01080.21360.07080.081720.0682-19.1109-28.817
31.3403-0.0593-0.51252.34190.76835.8295-0.0399-0.00110.1187-0.0340.01280.5043-0.3013-0.75840.0270.02220.0711-0.0010.35050.06060.131413.05266.4877-32.6105
41.23670.01780.5431.1714-0.12755.4448-0.0603-0.02320.35570.0766-0.0230.0538-0.7949-0.05960.08330.21910.06220.00060.0435-0.0020.105934.831721.8074-31.0198
51.4053-0.1242-0.36351.2727-0.09954.7758-0.01630.10870.0416-0.0467-0.0298-0.2487-0.22190.52840.04610.0225-0.03780.00860.17640.0040.049655.74035.3353-26.2643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 207
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 428
4X-RAY DIFFRACTION1E401
5X-RAY DIFFRACTION2B1 - 208
6X-RAY DIFFRACTION2B301
7X-RAY DIFFRACTION2A429
8X-RAY DIFFRACTION2B401 - 432
9X-RAY DIFFRACTION2C401
10X-RAY DIFFRACTION3C1 - 207
11X-RAY DIFFRACTION3C301
12X-RAY DIFFRACTION3B433
13X-RAY DIFFRACTION3C402 - 426
14X-RAY DIFFRACTION4D0 - 207
15X-RAY DIFFRACTION4A430
16X-RAY DIFFRACTION4C427 - 428
17X-RAY DIFFRACTION4D401 - 430
18X-RAY DIFFRACTION4E402
19X-RAY DIFFRACTION5E0 - 207
20X-RAY DIFFRACTION5E301
21X-RAY DIFFRACTION5A431 - 432
22X-RAY DIFFRACTION5E403 - 439
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ct1_2.parct1_2.top

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