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Yorodumi- PDB-2xys: Crystal structure of Aplysia californica AChBP in complex with st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xys | ||||||
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Title | Crystal structure of Aplysia californica AChBP in complex with strychnine | ||||||
Components | SOLUBLE ACETYLCHOLINE RECEPTOR | ||||||
Keywords | RECEPTOR / AMIDATION / CONFORMATIONAL FLEXIBILITY / CONOTOXIN / NEUROTOXIN / NICOTINIC / POSTSYNAPTIC NEUROTOXIN / RECEPTOR-TOXIN COMPLEX | ||||||
Function / homology | Function and homology information excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / 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: 1.909 Å | ||||||
Authors | Brams, M. / Pandya, A. / Kuzmin, D. / van Elk, R. / Krijnen, L. / Yakel, J.L. / Tsetlin, V. / Smit, A.B. / Ulens, C. | ||||||
Citation | Journal: Plos Biol. / Year: 2011 Title: A Structural and Mutagenic Blueprint for Molecular Recognition of Strychnine and D-Tubocurarine by Different Cys-Loop Receptors. Authors: Brams, M. / Pandya, A. / Kuzmin, D. / Van Elk, R. / Krijnen, L. / Yakel, J.L. / Tsetlin, V. / Smit, A.B. / Ulens, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xys.cif.gz | 441.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xys.ent.gz | 364.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xys_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 2xys_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 2xys_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 2xys_validation.cif.gz | 76 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xys ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xys | HTTPS FTP |
-Related structure data
Related structure data | 2xytC 2uz6S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.029, -0.004), Vector: |
-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) Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8 #2: Chemical | ChemComp-SY9 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.06 % / Description: NONE |
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Crystal grow | Details: 200 MM SODIUM ACETATE, 100 MM BISTRISPROPANE AT PH 8.5, 15.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→49.56 Å / Num. obs: 113796 / % possible obs: 98.2 % / Observed criterion σ(I): 1.3 / Redundancy: 5.6 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UZ6 Resolution: 1.909→44.608 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 19.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.347 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.909→44.608 Å
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Refine LS restraints |
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LS refinement shell |
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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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