+Open data
-Basic information
Entry | Database: PDB / ID: 6hz0 | ||||||
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Title | THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT K248A | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / PENTAMERIC TRANSMEMBRANE CHANNEL / ION CHANNEL. | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus PCC 7421 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å | ||||||
Authors | Hu, H.D. / Delarue, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Authors: Hu, H. / Ataka, K. / Menny, A. / Fourati, Z. / Sauguet, L. / Corringer, P.J. / Koehl, P. / Heberle, J. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hz0.cif.gz | 344.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hz0.ent.gz | 279.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hz0_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 6hz0_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 6hz0_validation.xml.gz | 64.7 KB | Display | |
Data in CIF | 6hz0_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/6hz0 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/6hz0 | HTTPS FTP |
-Related structure data
Related structure data | 6hy5C 6hy9C 6hyaC 6hyrC 6hyvC 6hywC 6hyxC 6hyzC 6hz1C 6hz3C 6hzwC 6i08C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 5 - 315 / Label seq-ID: 5 - 315
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36219.621 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus PCC 7421 (bacteria) Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #6: Sugar | ChemComp-LMT / |
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-Non-polymers , 5 types, 358 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PLC / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #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: 5.16 Å3/Da |
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Crystal grow | Temperature: 291 K / Method: evaporation Details: 12-14.5% PEG4K; 15% GLycerol; 400 mM NaSCN; 3% DMSO; 100mM NaAcetate pH 4. |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→49.14 Å / Num. obs: 94881 / % possible obs: 99.3 % / Redundancy: 5.3 % / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.75→2.8 Å |
-Processing
Software |
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Refinement | Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 15.763 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.255 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→20 Å
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Refine LS restraints |
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