+Open data
-Basic information
Entry | Database: PDB / ID: 2byn | ||||||
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Title | Crystal structure of apo AChBP from Aplysia californica | ||||||
Components | SOLUBLE ACETYLCHOLINE RECEPTOR | ||||||
Keywords | RECEPTOR / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR / SOLUBLE ACETYLCHOLINE RECEPTOR / CONFORMATIONAL FLEXIBILITY | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structures of Aplysia Achbp Complexes with Nicotinic Agonists and Antagonists Reveal Distinctive Binding Interfaces and Conformations. Authors: Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2byn.cif.gz | 245.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2byn.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 2byn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2byn ftp://data.pdbj.org/pub/pdb/validation_reports/by/2byn | HTTPS FTP |
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-Related structure data
Related structure data | 2bypC 2byqC 2byrC 2bysC 1ux2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25852.744 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / Cell: SENSORY CELL / References: UniProt: Q8WSF8 #2: Chemical | ChemComp-PG4 / #3: Chemical | ChemComp-1PE / | #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | pH: 5.6 Details: 12-14% PEG 4000, 0.1 M SODIUM CITRATE, PH 5.6, 20% ISOPROPANOL, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 97846 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UX2 Resolution: 2.02→40.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.514 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→40.03 Å
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Refine LS restraints |
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