+Open data
-Basic information
Entry | Database: PDB / ID: 6sh0 | ||||||
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Title | Crystal structure of AcAChBP in complex with anatoxin | ||||||
Components | Acetylcholine binding protein | ||||||
Keywords | SIGNALING PROTEIN / toxin / acetylcholine binding protein | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aplysia californica (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hunter, W.N. / Dawson, A. / Parker, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (-)-hosieine-A Authors: Parker, H.P. / Dawson, A. / Jones, M.J. / Yan, R. / Ouyang, J. / Hong, R. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sh0.cif.gz | 432.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sh0.ent.gz | 354.8 KB | Display | PDB format |
PDBx/mmJSON format | 6sh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/6sh0 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/6sh0 | HTTPS FTP |
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-Related structure data
Related structure data | 6sgvC 2xysS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 19 molecules ABCDEFGHIJ
#1: Protein | Mass: 28326.750 Da / Num. of mol.: 10 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: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 982 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-4P0 / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Reservoir solution: 8% PEG 4K, 0.1 M NaOAc pH 4.6 Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 4mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 15, 2017 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→127.87 Å / Num. obs: 119138 / % possible obs: 99.5 % / Redundancy: 11.8 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.089 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5811 / CC1/2: 0.813 / Rpim(I) all: 0.286 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xys Resolution: 2.5→59.77 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.279 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.419 / ESU R Free: 0.292 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.47 Å2 / Biso mean: 26.137 Å2 / Biso min: 4.96 Å2
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Refinement step | Cycle: final / Resolution: 2.5→59.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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