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- PDB-5oan: Crystal structure of mutant AChBP in complex with glycine (T53F, ... -

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Basic information

Entry
Database: PDB / ID: 5oan
TitleCrystal structure of mutant AChBP in complex with glycine (T53F, Q74R, Y110A, I135S, G162E, S206CCP_KGTG)
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / receptor / acetylcholine binding
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
ACETATE ION / GLYCINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.
CitationJournal: Iucrj / Year: 2019
Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.
Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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: 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)142,32119
Polymers141,5485
Non-polymers77314
Water4,504250
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17250 Å2
ΔGint-136 kcal/mol
Surface area41610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.919, 100.266, 165.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA20 - 22420 - 224
21ARGARGBB20 - 22420 - 224
12ARGARGAA20 - 22420 - 224
22ARGARGCC20 - 22420 - 224
13ARGARGAA20 - 22420 - 224
23ARGARGDD20 - 22420 - 224
14ARGARGAA20 - 22420 - 224
24ARGARGEE20 - 22420 - 224
15GLYGLYBB - H20 - 60120
25HISHISCC20 - 24920 - 248
16GLYGLYBB - H20 - 60120
26GLYGLYDD - N20 - 60120
17ARGARGBB20 - 22520 - 225
27ARGARGEE20 - 22520 - 225
18HISHISCC20 - 24520 - 244
28PHEPHEDD20 - 23120 - 231
19ARGARGCC20 - 22520 - 225
29ARGARGEE20 - 22520 - 225
110ARGARGDD20 - 22520 - 225
210ARGARGEE20 - 22520 - 225

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 28309.680 Da / Num. of mol.: 5
Mutation: T53F, Q74R, Y110A, I135S, G162E, S206K, C207G, C208T, P209G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Reservoir solution:2 M sodium formate, 0.1 M sodium acetate pH 4.6 . Protein buffer: 50 mM tris, 250 mM NaCl, 0.1 M glycine

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54157 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 15, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54157 Å / Relative weight: 1
ReflectionResolution: 2.6→32.9 Å / Num. obs: 46736 / % possible obs: 99.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OAD

5oad


Resolution: 2.6→32.9 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.026 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.276 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2381 5.1 %RANDOM
Rwork0.202 ---
obs0.204 44310 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8351 0 45 250 8646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028698
X-RAY DIFFRACTIONr_bond_other_d0.0060.027763
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.94911841
X-RAY DIFFRACTIONr_angle_other_deg0.931318048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47851058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79224.065428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7671560
X-RAY DIFFRACTIONr_chiral_restr0.0840.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021826
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_it1.982.7994203
X-RAY DIFFRACTIONr_mcbond_other1.982.7994201
X-RAY DIFFRACTIONr_mcangle_it3.4844.1745230
X-RAY DIFFRACTIONr_mcangle_other3.4844.1755231
X-RAY DIFFRACTIONr_scbond_it1.7982.9614495
X-RAY DIFFRACTIONr_scbond_other1.7982.9614496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1294.3486600
X-RAY DIFFRACTIONr_long_range_B_refined6.17531.0519195
X-RAY DIFFRACTIONr_long_range_B_other6.16531.0579184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A130760.06
12B130760.06
21A130960.06
22C130960.06
31A131060.05
32D131060.05
41A130880.05
42E130880.05
51B133180.06
52C133180.06
61B132280.06
62D132280.06
71B131320.06
72E131320.06
81C132120.06
82D132120.06
91C132200.05
92E132200.05
101D132180.05
102E132180.05
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 183 -
Rwork0.321 3198 -
obs--99.82 %

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