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- PDB-4zru: X-ray crystal structure of Lymnaea stagnalis acetylcholine bindin... -

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Basic information

Entry
Database: PDB / ID: 4zru
TitleX-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in complex with 3-[2-[(2S)-pyrrolidin-2-yl]ethynyl]pyridine (TI-5180)
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE BINDING PROTEIN / nicotinic / acetylcholine / Ls-AChBP
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
PHOSPHATE ION / 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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, and Structural Features of a High-Affinity, Non-selective NNR Ligand-AChBP Co-crystal Structure
Authors: Talley, T.T.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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_keywords.text

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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)251,26730
Polymers248,59510
Non-polymers2,67220
Water27,9231550
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)125,63315
Polymers124,2975
Non-polymers1,33610
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15940 Å2
ΔGint-117 kcal/mol
Surface area39000 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)125,63315
Polymers124,2975
Non-polymers1,33610
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16140 Å2
ΔGint-118 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.910, 108.870, 122.700
Angle α, β, γ (deg.)90.000, 95.310, 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.: 10 / 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): HEK293S GnTI- / 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-TI9 / 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine


Mass: 172.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C11H12N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1550 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.51 %
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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2010
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: 1.854→92.511 Å / Num. obs: 203061 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 23.75 Å2 / Rmerge F obs: 0.098 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.066 / Χ2: 1.004 / Net I/σ(I): 17.62 / Num. measured all: 1095391
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.854-1.90.8270.6981.895364515271129650.80184.9
1.9-1.950.560.512.86204014881138870.57993.3
1.95-2.010.3710.3714.37454014494143220.41398.8
2.01-2.070.2750.35.67897914071140290.33199.7
2.07-2.140.2130.2367.187691013633135870.2699.7
2.14-2.210.1690.1928.817402613157131130.21299.7
2.21-2.290.1360.15410.857169612724126760.1799.6
2.29-2.390.1090.12912.716908312259122200.14299.7
2.39-2.490.0910.10715.016602011737117210.11899.9
2.49-2.620.0750.09117.396320611234112040.199.7
2.62-2.760.0590.07320.936020410706106720.0899.7
2.76-2.930.0470.06124.155694210140101110.06799.7
2.93-3.130.0350.04829.1253027951794880.05399.7
3.13-3.380.0270.03933.7248707885888310.04399.7
3.38-3.70.0220.03238.4343973815581190.03599.6
3.7-4.140.0180.02941.4639824739873700.03299.6
4.14-4.780.0160.02744.7435434655865320.0399.6
4.78-5.850.0170.02944.0830129554655220.03299.6
5.85-8.270.0170.02843.7723990431442980.03199.6
8.270.0130.02248.0713016241723940.02599

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Processing

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

4zjt

4zk1


Resolution: 1.9→90 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 20.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 9550 5.04 %
Rwork0.1709 179972 -
obs0.1726 189522 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.04 Å2 / Biso mean: 26.2217 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 1.9→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15908 0 300 1550 17758
Biso mean--25.07 33.3 -
Num. residues----2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716527
X-RAY DIFFRACTIONf_angle_d1.09522622
X-RAY DIFFRACTIONf_chiral_restr0.0442643
X-RAY DIFFRACTIONf_plane_restr0.0052902
X-RAY DIFFRACTIONf_dihedral_angle_d12.1735798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.29533160.23865465578191
1.9216-1.94420.27612870.21725802608995
1.9442-1.96790.26673220.19735789611197
1.9679-1.99280.23693140.1935981629599
1.9928-2.01910.24423240.187560746398100
2.0191-2.04670.2412820.183360126294100
2.0467-2.0760.21953250.179160066331100
2.076-2.10690.24473160.182460096325100
2.1069-2.13990.25143340.179859706304100
2.1399-2.1750.21743380.177960366374100
2.175-2.21250.2293190.185160036322100
2.2125-2.25270.2173150.178359906305100
2.2527-2.2960.223140.174960216335100
2.296-2.34290.21373150.172960366351100
2.3429-2.39380.19992950.186960726367100
2.3938-2.44950.24593310.179659896320100
2.4495-2.51080.223250.180560536378100
2.5108-2.57870.24853240.180959936317100
2.5787-2.65460.1763300.17260686398100
2.6546-2.74030.2143340.174359786312100
2.7403-2.83820.21993250.183859806305100
2.8382-2.95190.22033350.178160366371100
2.9519-3.08620.21752970.17660866383100
3.0862-3.24890.19472950.176260476342100
3.2489-3.45250.21182690.167860926361100
3.4525-3.71910.19183020.158360816383100
3.7191-4.09330.16583330.149160416374100
4.0933-4.68560.15783630.134360276390100
4.6856-5.90330.16643150.154260946409100
5.9033-92.62110.20173560.18426141649799

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