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Yorodumi- PDB-2y58: Fragment growing induces conformational changes in acetylcholine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y58 | ||||||
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Title | Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Compound 6) | ||||||
Components | SOLUBLE ACETYLCHOLINE RECEPTOR | ||||||
Keywords | RECEPTOR | ||||||
Function / homology | Function and homology information acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | APLYSIA CALIFORNICA (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Rucktooa, P. / Edink, E. / deEsch, I.J.P. / Sixma, T.K. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis. Authors: Edink, E. / Rucktooa, P. / Retra, K. / Akdemir, A. / Nahar, T. / Zuiderveld, O. / Van Elk, R. / Janssen, E. / Van Nierop, P. / Van Muijlwijk-Koezen, J. / Smit, A.B. / Sixma, T.K. / Leurs, R. / De Esch, I.J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y58.cif.gz | 422.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y58.ent.gz | 352.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y58_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2y58_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2y58_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 2y58_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y58 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y58 | HTTPS FTP |
-Related structure data
Related structure data | 2y54C 2y56C 2y57C 2c9tS 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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Unit cell |
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-Components
#1: Protein | Mass: 24688.578 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare) Plasmid: PFASTBAC1 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8 #2: Chemical | ChemComp-V38 / [( #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / |
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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: 3.48 Å3/Da / Density % sol: 64.73 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.1M MMT PH 7.0, 1.4M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 29, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→14.53 Å / Num. obs: 25505 / % possible obs: 99.6 % / Observed criterion σ(I): 2.05 / Redundancy: 4.81 % / Biso Wilson estimate: 72.25 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.81 |
Reflection shell | Resolution: 3.25→3.33 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.05 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C9T Resolution: 3.25→47.7 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9159 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 71.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→47.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.38 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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