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Yorodumi- PDB-4qh5: The GLIC pentameric Ligand-Gated Ion Channel (wild-type) crystall... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qh5 | ||||||
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Title | The GLIC pentameric Ligand-Gated Ion Channel (wild-type) crystallized in phosphate buffer | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / pentameric ligand gated ion channel | ||||||
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 Å | ||||||
Authors | Fourati, Z. / Delarue, M. / Sauguet, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural characterization of potential modulation sites in the extracellular domain of the prokaryotic pentameric proton-gated ion channel GLIC Authors: Fourati, Z. / Sauguet, L. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qh5.cif.gz | 633.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qh5.ent.gz | 533.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/4qh5 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/4qh5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36220.672 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #2: Sugar | ChemComp-LMT / |
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-Non-polymers , 4 types, 67 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / #5: Chemical | #6: 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: 5.27 Å3/Da / Density % sol: 76.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 400 mM Sodium Isothiocyanate, 100 mM Sodium acetate, 16% glycerol, 12-15% PEG4000, 2% DMSO, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.93 Å / Num. all: 211949 / Num. obs: 71886 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 89.88 Å2 |
Reflection shell | Resolution: 3→3.16 Å / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.9041 / Cor.coef. Fo:Fc free: 0.9005 / SU R Cruickshank DPI: 0.491 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 108.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.506 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 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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