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- PDB-4zr6: Lymnaea Stagnalis Acetylcholine Binding Protein in Complex with 3... -

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Basic information

Entry
Database: PDB / ID: 4zr6
TitleLymnaea Stagnalis Acetylcholine Binding Protein in Complex with 3-[(4E)-4-[(3-methylimidazol-4-yl)methylene]-2,3-dihydropyrrol-5-yl]pyridine
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE BINDING PROTEIN / acetylcholine / nicotinic / AChBP / Myosmine
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / 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-4QW / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBobango, J. / Bryant, D. / Denton, T.T. / Talley, T.T.
CitationJournal: To be Published
Title: Structure-guided design and analysis of arylidene anabaseines and myosmines
Authors: Denton, T.T. / Bobango, J. / Talley, T.T.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)125,48910
Polymers124,2975
Non-polymers1,1915
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-64 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.924, 78.100, 120.502
Angle α, β, γ (deg.)90.000, 102.320, 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.: 5 / Fragment: UNP residues 20-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Cell line (production host): HEK 293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P58154
#2: Chemical
ChemComp-4QW / 3-{(4E)-4-[(1-methyl-1H-imidazol-5-yl)methylidene]-3,4-dihydro-2H-pyrrol-5-yl}pyridine


Mass: 238.288 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H14N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% v/v MPD

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.511→47.007 Å / Num. all: 41678 / Num. obs: 41678 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 25.2
Reflection shell
Resolution (Å)CC1/2Rpim(I) allΧ2
2.5-2.540.8190.3680.56
2.54-2.590.8660.320.583
2.59-2.640.8940.3180.595
2.64-2.690.9290.2920.611
2.69-2.750.9370.2810.642
2.75-2.820.9310.2610.692
2.82-2.890.9410.2530.736
2.89-2.960.9620.2270.801
2.96-3.050.9680.1930.991
3.05-3.150.9630.181.158
3.15-3.260.9590.1531.497
3.26-3.390.9790.1331.818
3.39-3.550.9750.1152.203
3.55-3.730.9780.1052.735
3.73-3.970.9780.0912.919
3.97-4.270.9810.0693.518
4.27-4.70.9880.063.782
4.7-5.380.9870.0573.858
5.38-6.780.9890.0543.639
6.78-500.9950.0363.877

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4ZJT & 4ZK1

4zjt

4zk1


Resolution: 2.6→44.259 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1854 4.8 %
Rwork0.2101 36782 -
obs0.2128 38636 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 46.5787 Å2 / Biso min: 19.15 Å2
Refinement stepCycle: final / Resolution: 2.6→44.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 160 7 7363
Biso mean--46.61 34.79 -
Num. residues----983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017473
X-RAY DIFFRACTIONf_angle_d1.2310285
X-RAY DIFFRACTIONf_chiral_restr0.0451242
X-RAY DIFFRACTIONf_plane_restr0.0051305
X-RAY DIFFRACTIONf_dihedral_angle_d13.6672444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.67030.31611470.257928142961
2.6703-2.74890.34421400.251128082948
2.7489-2.83760.32151440.253527822926
2.8376-2.9390.34231420.256328132955
2.939-3.05660.35791350.250828462981
3.0566-3.19570.321500.241927892939
3.1957-3.36410.2851370.220728552992
3.3641-3.57480.26171410.211728232964
3.5748-3.85070.23741470.200128172964
3.8507-4.23790.25191370.179728192956
4.2379-4.85050.2081390.175428452984
4.8505-6.10850.24281500.198928563006
6.1085-44.26540.25151450.209229153060

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