+Open data
-Basic information
Entry | Database: PDB / ID: 6hpp | ||||||
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Title | X-ray structure of GLIC in complex with propionate | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / Pentameric Ligand-Gated Ion channel | ||||||
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: 3.2 Å | ||||||
Authors | Fourati, Z. / Delarue, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. 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 | 6hpp.cif.gz | 633.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hpp.ent.gz | 552 KB | Display | PDB format |
PDBx/mmJSON format | 6hpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hpp ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hpp | 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
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36277.723 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 #4: Sugar | ChemComp-LMT / |
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-Non-polymers , 4 types, 45 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #5: Chemical | ChemComp-PPI / #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: 5.19 Å3/Da / Density % sol: 76.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Na-propionate, pH 4 400 mM NaIsothiocyanate 12-15% PEG4000 2% DMSO 15% glycreol |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 61051 / % possible obs: 97.12 % / Redundancy: 3.6 % / Biso Wilson estimate: 79.69 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.2→3.28 Å / CC1/2: 0.413 |
-Processing
Software |
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Refinement | Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.713 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.586 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.295
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Displacement parameters | Biso mean: 113.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.28 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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