+Open data
-Basic information
Entry | Database: PDB / ID: 6f11 | ||||||
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Title | GLIC mutant D86A | ||||||
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: 2.95 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f11.cif.gz | 642.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f11.ent.gz | 554 KB | Display | PDB format |
PDBx/mmJSON format | 6f11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f11 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f11 | HTTPS FTP |
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-Related structure data
Related structure data | 6f0iC 6f0jC 6f0mC 6f0nC 6f0rC 6f0uC 6f0vC 6f0zC 6f10C 6f12C 6f13C 6f15C 6f16C 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
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36233.711 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 #5: Sugar | ChemComp-LMT / |
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-Non-polymers , 5 types, 61 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-ACT / #6: Chemical | #7: 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: 5.25 Å3/Da / Density % sol: 76.58 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 100 mM NaAcetate pH4 400 mM NaSCN 12-15% PEG 4000 15% glycerol 3%DMSO |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→49.44 Å / Num. obs: 77611 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 90.75 Å2 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.95→3.01 Å |
-Processing
Software |
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Refinement | Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.9132 / SU R Cruickshank DPI: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.366 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.261
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Displacement parameters | Biso mean: 80.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.03 Å / Total num. of bins used: 20
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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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