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Yorodumi- PDB-5l47: X-ray structure of the 2-22' locally-closed mutant of GLIC in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l47 | ||||||
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Title | X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with cyanoselenobarbital (seleniated barbiturate) | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Reinholds Ruza, R. / Fourati, Z. / Delarue, M. | ||||||
Funding support | France, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State. Authors: Fourati, Z. / Ruza, R.R. / Laverty, D. / Drege, E. / Delarue-Cochin, S. / Joseph, D. / Koehl, P. / Smart, T. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l47.cif.gz | 318.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l47.ent.gz | 261.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/5l47 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l47 | HTTPS FTP |
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-Related structure data
Related structure data | 5l4eC 5l4hC 3tlvS S: Starting model for refinement 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 , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 36225.605 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter (bacteria) / Strain: PCC 7421 / Tissue: Memrane / Gene: glvI, glr4197 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q7NDN8 |
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-Non-polymers , 6 types, 123 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-6JA / | #6: Chemical | ChemComp-D12 / | #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: 5.07 Å3/Da / Density % sol: 75.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100 mM Na Acetate pH4, 200 mM Na SCN, 12-15% PEG4000, 3% DMSO, 16% glycerol PH range: 4-5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 72625 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 93.49 Å2 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.99→3.15 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TLV.pdb Resolution: 3.3→49 Å / Cor.coef. Fo:Fc: 0.8344 / Cor.coef. Fo:Fc free: 0.8028 / SU R Cruickshank DPI: 0.607 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.535 / SU Rfree Blow DPI: 0.3 / SU Rfree Cruickshank DPI: 0.313
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Displacement parameters | Biso mean: 89.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.448 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.3→49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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