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- PDB-5bp0: X-ray crystal structure of Lymnaea stagnalis acetylcholine bindin... -

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Basic information

Entry
Database: PDB / ID: 5bp0
TitleX-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 5-Fluoronicotine (TI-4650)
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / nicotine / acetylcholine
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
5-fluoronicotine / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
CitationJournal: To Be Published
Title: Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs
Authors: Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)251,42930
Polymers248,59510
Non-polymers2,83420
Water5,927329
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)126,11617
Polymers124,2975
Non-polymers1,81812
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-102 kcal/mol
Surface area39110 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)125,31313
Polymers124,2975
Non-polymers1,0168
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-109 kcal/mol
Surface area39170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.470, 129.040, 122.430
Angle α, β, γ (deg.)90.00, 106.28, 90.00
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.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Cell line (production host): HEK GNT1- / Production host: Homo sapiens (human) / References: UniProt: P58154
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FN1 / 5-fluoronicotine / 3-fluoro-5-[(2S)-1-methylpyrrolidin-2-yl]pyridine


Mass: 180.222 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13FN2
#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.: 329 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.26 M ammonium phosphate, 35% glycerol

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→55.16 Å / Num. obs: 95633 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 42.56 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.4-2.466.50.82.74498669130.35198.2
10.73-55.167.10.04740.7793311160.01998.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia20.3.3.3data scaling
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4ZJT & 4ZK1

4zjt

4zk1


Resolution: 2.4→55.16 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 4792 5.01 %
Rwork0.198 --
obs0.2 95579 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.35 Å2
Refinement stepCycle: LAST / Resolution: 2.4→55.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15410 0 182 329 15921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115957
X-RAY DIFFRACTIONf_angle_d1.27221873
X-RAY DIFFRACTIONf_dihedral_angle_d14.0395473
X-RAY DIFFRACTIONf_chiral_restr0.0472584
X-RAY DIFFRACTIONf_plane_restr0.0062802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.32841650.27622913X-RAY DIFFRACTION97
2.4273-2.45580.3141670.24992962X-RAY DIFFRACTION99
2.4558-2.48580.32611690.25913012X-RAY DIFFRACTION99
2.4858-2.51720.36171820.27082985X-RAY DIFFRACTION99
2.5172-2.55040.3261540.24813049X-RAY DIFFRACTION100
2.5504-2.58530.33091440.23963051X-RAY DIFFRACTION100
2.5853-2.62220.27231680.23462959X-RAY DIFFRACTION99
2.6222-2.66140.36071340.23143079X-RAY DIFFRACTION100
2.6614-2.7030.291770.22332948X-RAY DIFFRACTION99
2.703-2.74730.28021460.21643039X-RAY DIFFRACTION99
2.7473-2.79460.30641770.22762997X-RAY DIFFRACTION99
2.7946-2.84550.2951700.22983002X-RAY DIFFRACTION99
2.8455-2.90020.30251540.2312973X-RAY DIFFRACTION100
2.9002-2.95940.27591760.21833057X-RAY DIFFRACTION100
2.9594-3.02370.29841290.20183024X-RAY DIFFRACTION100
3.0237-3.09410.24131580.20373041X-RAY DIFFRACTION100
3.0941-3.17140.27851740.21293034X-RAY DIFFRACTION100
3.1714-3.25720.27681540.20753008X-RAY DIFFRACTION100
3.2572-3.3530.26121580.22213062X-RAY DIFFRACTION100
3.353-3.46120.2821670.21032997X-RAY DIFFRACTION100
3.4612-3.58490.24591580.19863050X-RAY DIFFRACTION100
3.5849-3.72840.24361510.19353065X-RAY DIFFRACTION100
3.7284-3.8980.23621710.18413006X-RAY DIFFRACTION100
3.898-4.10350.22681540.1853066X-RAY DIFFRACTION100
4.1035-4.36050.22281510.16333073X-RAY DIFFRACTION100
4.3605-4.6970.18951490.1483024X-RAY DIFFRACTION100
4.697-5.16940.19541450.16163087X-RAY DIFFRACTION100
5.1694-5.91660.19451570.17993072X-RAY DIFFRACTION100
5.9166-7.45140.231730.20113056X-RAY DIFFRACTION100
7.4514-55.17470.21141600.1933096X-RAY DIFFRACTION99

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