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Yorodumi- PDB-5lid: X-ray structure of a pentameric ligand gated ion channel from Erw... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lid | ||||||
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Title | X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromopromazine | ||||||
Components | Cys-loop ligand-gated ion channel | ||||||
Keywords | TRANSPORT PROTEIN / ligand-gated ion channel | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Dickeya chrysanthemi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Nys, M. / Wijckmans, E. / Farinha, A. / Brams, M. / Spurny, R. / Ulens, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine. Authors: Nys, M. / Wijckmans, E. / Farinha, A. / Yoluk, O. / Andersson, M. / Brams, M. / Spurny, R. / Peigneur, S. / Tytgat, J. / Lindahl, E. / Ulens, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lid.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lid.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5lid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5lid ftp://data.pdbj.org/pub/pdb/validation_reports/li/5lid | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 35383.367 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7 #2: Chemical | ChemComp-6XY / |
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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: 4.27 Å3/Da / Density % sol: 71.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM ammonium sulfate, 50 mM ADA pH 6.5, 9-12 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91983 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→49.54 Å / Num. obs: 69231 / % possible obs: 99.8 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 11.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→49.537 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 26.98 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→49.537 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain 'd' and resid ' 1 ' and name 'BR ' and altloc ' ' |