+Open data
-Basic information
Entry | Database: PDB / ID: 6f13 | ||||||
---|---|---|---|---|---|---|---|
Title | GLIC mutant E75A | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Hu, H.D. / Delarue, M. | ||||||
Citation | Journal: PLoS Biol. / Year: 2017 Title: Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel. Authors: Nemecz, A. / Hu, H. / Fourati, Z. / Van Renterghem, C. / Delarue, M. / Corringer, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f13.cif.gz | 673.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f13.ent.gz | 562.8 KB | Display | PDB format |
PDBx/mmJSON format | 6f13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f13 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f13 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6f0iC 6f0jC 6f0mC 6f0nC 6f0rC 6f0uC 6f0vC 6f0zC 6f10C 6f11C 6f12C 6f15C 6f16C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36219.688 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 #6: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 5 types, 335 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PLC / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.22 Å3/Da / Density % sol: 76.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation Details: 100 mM NaAcetate pH 4 200mM NaSCN 12-15% PEG4000 15% glycerol 3%DMSO |
-Data collection
Diffraction | Mean temperature: 190 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.1 Å / Num. obs: 100065 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 69.64 Å2 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.75 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.7→49.1 Å / Cor.coef. Fo:Fc: 0.9005 / Cor.coef. Fo:Fc free: 0.9056 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.22
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.96 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.359 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→49.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|