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

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Basic information

Entry
Database: PDB / ID: 4zjt
TitleX-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE BINDING PROTEIN / nicotinic / AChBP / receptor / Anabaseine
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-4P6 / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBobango, J. / Wu, J. / Talley, T.T.
CitationJournal: To Be Published
Title: X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)
Authors: Bobango, J. / Wu, J. / Talley, T.T.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 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
Revision 1.2Nov 20, 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
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)252,08830
Polymers248,59510
Non-polymers3,49320
Water11,818656
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)126,04415
Polymers124,2975
Non-polymers1,74710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16910 Å2
ΔGint-107 kcal/mol
Surface area41250 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)126,04415
Polymers124,2975
Non-polymers1,74710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17320 Å2
ΔGint-108 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.842, 127.603, 122.469
Angle α, β, γ (deg.)90.000, 110.450, 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-4P6 / (3E)-3-(thiophen-2-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine / 2-thiophenylmethylene anabaseine


Mass: 254.350 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H14N2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011
Diffraction measurementDetails: 1.00 degrees, 1.0 sec, detector distance 250.00 mm
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.077 / Number: 1708039
ReflectionResolution: 1.74→50 Å / Num. obs: 248133 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/av σ(I): 22.167 / Net I/σ(I): 23.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.035 / Mean I/σ(I) obs: 1.237 / Rsym value: 0.688 / % possible all: 68.5
Cell measurementReflection used: 1708039

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1YI5, 1UV6, 1UW6, 1UX2, 2ZJU, 2ZJV

1yi5

1uv6

1uw6

1ux2

2zju

2zjv


Resolution: 1.85→49.985 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1738 0.83 %
Rwork0.1888 207430 -
obs0.1891 209168 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.68 Å2 / Biso mean: 26.4473 Å2 / Biso min: 12.21 Å2
Refinement stepCycle: final / Resolution: 1.85→49.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16540 0 370 656 17566
Biso mean--28.28 27.42 -
Num. residues----2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717190
X-RAY DIFFRACTIONf_angle_d1.33223480
X-RAY DIFFRACTIONf_chiral_restr0.0422681
X-RAY DIFFRACTIONf_plane_restr0.0053104
X-RAY DIFFRACTIONf_dihedral_angle_d13.016100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90440.32141440.2572167841692897
1.9044-1.96590.25441440.2186171511729599
1.9659-2.03620.26191430.20311724217385100
2.0362-2.11770.27131410.2031722517366100
2.1177-2.21410.24051450.20081732117466100
2.2141-2.33080.25281470.20271728317430100
2.3308-2.47680.26751470.20451728217429100
2.4768-2.66810.25531440.21281739417538100
2.6681-2.93650.21531460.20681735817504100
2.9365-3.36140.25081450.19581737617521100
3.3614-4.23470.17671450.16511745017595100
4.2347-50.00370.18491470.15631756417711100

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