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Yorodumi- PDB-3rqu: Crystal structure of a prokaryotic pentameric ligand-gated ion ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rqu | ||||||
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Title | Crystal structure of a prokaryotic pentameric ligand-gated ion channel, ELIC | ||||||
Components | ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi | ||||||
Keywords | TRANSPORT PROTEIN / ion channel / membrane | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Dickeya dadantii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 Å | ||||||
Authors | Pan, J.J. / Chen, Q. / Yoshida, K. / Cohen, A. / Kong, X.P. / Xu, Y. / Tang, P. | ||||||
Citation | Journal: Nat Commun / Year: 2012 Title: Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine. Authors: Pan, J. / Chen, Q. / Willenbring, D. / Yoshida, K. / Tillman, T. / Kashlan, O.B. / Cohen, A. / Kong, X.P. / Xu, Y. / Tang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rqu.cif.gz | 620 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rqu.ent.gz | 512.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/3rqu ftp://data.pdbj.org/pub/pdb/validation_reports/rq/3rqu | HTTPS FTP |
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-Related structure data
Related structure data | 3rqwC 2vl0S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 36879.000 Da / Num. of mol.: 10 / Fragment: UNP residues 22-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4 #2: Chemical | ChemComp-MES / #3: Chemical | ChemComp-GOL / #4: 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: 4.04 Å3/Da / Density % sol: 69.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 12% PEG4000, 0.1 M MES, 0.2 M ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.087→29.8 Å / Num. obs: 104053 / % possible obs: 97.4 % / Observed criterion σ(I): 2.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VL0 Resolution: 3.089→24.99 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 28.06 / 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: 61.463 Å2 / ksol: 0.272 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.089→24.99 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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