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Yorodumi- PDB-4zzb: The GLIC pentameric Ligand-Gated Ion Channel Locally-closed form ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zzb | ||||||
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Title | The GLIC pentameric Ligand-Gated Ion Channel Locally-closed form complexed to xenon | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN | ||||||
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 8105 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å | ||||||
Authors | Sauguet, L. / Fourati, Z. / Prange, T. / Delarue, M. / Colloc'h, N. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. Authors: Sauguet, L. / Fourati, Z. / Prange, T. / Delarue, M. / Colloc'h, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zzb.cif.gz | 624.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zzb.ent.gz | 544.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zzb_validation.pdf.gz | 639.7 KB | Display | wwPDB validaton report |
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Full document | 4zzb_full_validation.pdf.gz | 655.9 KB | Display | |
Data in XML | 4zzb_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 4zzb_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/4zzb ftp://data.pdbj.org/pub/pdb/validation_reports/zz/4zzb | HTTPS FTP |
-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, 6 molecules ABCDE
#1: Protein | Mass: 36239.633 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C27S K33C L246C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus PCC 8105 (bacteria) Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #2: Sugar | ChemComp-LMT / | |
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-Non-polymers , 4 types, 37 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-XE / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 12-15 % PEG4000 0.1M Na Acetate pH4 0.4M NaSCN 15% glycerol 5% DMSO PH range: 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.2 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→48.62 Å / Num. obs: 47834 / % possible obs: 98.4 % / Redundancy: 3 % / Biso Wilson estimate: 99.54 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.8 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.8844 / Cor.coef. Fo:Fc free: 0.8968 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 5.326 / SU Rfree Blow DPI: 0.372
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Displacement parameters | Biso mean: 127.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.845 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.49 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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