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- PDB-4zk1: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 4zk1
TitleCrystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein (LsAChBP) in Complex with 3-Pyrrolylmethylene Anabaseine
ComponentsAcetylcholine-binding protein
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / nicotinic / 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-4P7 / PHOSPHATE ION / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBobango, J. / Wu, J. / Talley, T.T.
CitationJournal: To be Published
Title: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein (LsAChBP) in Complex with 3-Pyrrolylmethylene Anabaseine
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 1.2Oct 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: 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)251,91830
Polymers248,59510
Non-polymers3,32320
Water14,484804
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)125,95915
Polymers124,2975
Non-polymers1,66110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17120 Å2
ΔGint-107 kcal/mol
Surface area41290 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)125,95915
Polymers124,2975
Non-polymers1,66110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16950 Å2
ΔGint-104 kcal/mol
Surface area41580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.045, 127.998, 122.600
Angle α, β, γ (deg.)90.000, 110.220, 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-4P7 / (3E)-3-(1H-pyrrol-3-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine / 3-pyrrolylmethylene anabaseine


Mass: 237.300 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H15N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
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: 80 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, 2.0 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: 0.065 / Number: 1844560
ReflectionResolution: 1.75→50 Å / Num. obs: 250015 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 44.68 / Net I/σ(I): 47.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.921 / Rsym value: 0.389 / % possible all: 96.2
Cell measurementReflection used: 1844560

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
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: 1.75→42.604 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1997 0.8 %
Rwork0.1918 247244 -
obs0.192 249241 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.55 Å2 / Biso mean: 24.0972 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.75→42.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16401 0 380 804 17585
Biso mean--26.07 27.2 -
Num. residues----2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617045
X-RAY DIFFRACTIONf_angle_d1.29523309
X-RAY DIFFRACTIONf_chiral_restr0.0422682
X-RAY DIFFRACTIONf_plane_restr0.0053076
X-RAY DIFFRACTIONf_dihedral_angle_d12.4045993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79370.25321370.2211169831712096
1.7937-1.84220.23481430.21031757717720100
1.8422-1.89640.23451480.19811763217780100
1.8964-1.95770.22511400.19011772417864100
1.9577-2.02760.20761400.18741760917749100
2.0276-2.10880.25451450.19571770317848100
2.1088-2.20480.21341440.19661771517859100
2.2048-2.3210.24791420.20371766417806100
2.321-2.46640.23851420.20431774117883100
2.4664-2.65680.24031420.21421767817820100
2.6568-2.92410.25521430.21161773717880100
2.9241-3.34710.23561440.20271775817902100
3.3471-4.21640.18361440.17361779517939100
4.2164-42.61630.17481430.16841792818071100

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