[English] 日本語
Yorodumi- PDB-6emx: X-ray structure of the N15'C mutant of GLIC in complex with bromoform -
+Open data
-Basic information
Entry | Database: PDB / ID: 6emx | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the N15'C mutant of GLIC in complex with bromoform | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / potassium channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Fourati, Z. / Delarue, M. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Authors: Fourati, Z. / Howard, R.J. / Heusser, S.A. / Hu, H. / Ruza, R.R. / Sauguet, L. / Lindahl, E. / Delarue, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6emx.cif.gz | 635.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6emx.ent.gz | 540.5 KB | Display | PDB format |
PDBx/mmJSON format | 6emx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/6emx ftp://data.pdbj.org/pub/pdb/validation_reports/em/6emx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37407.938 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria) Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MBR / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.98 Å3/Da / Density % sol: 75.31 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 12-14% PEGK 400mM NaSCN 100 mM NaAcetate pH 4 15% glycerol 3% DMSO |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49 Å / Num. obs: 60179 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.61 Å2 / Net I/σ(I): 8.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.62 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.855 / SU R Cruickshank DPI: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.768 / SU Rfree Blow DPI: 0.377 / SU Rfree Cruickshank DPI: 0.396
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.88 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→28.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.28 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|