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Yorodumi- PDB-4hfc: The GLIC pentameric Ligand-Gated Ion Channel F14'A ethanol-sensit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hfc | ||||||
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Title | The GLIC pentameric Ligand-Gated Ion Channel F14'A ethanol-sensitive mutant complexed to 2-bromo-ethanol | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Sauguet, L. / Howard, R.J. / Malherbe, L. / Lee, U.S. / Corringer, P.J. / Harris, R.A. / Delarue, M. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel. Authors: Sauguet, L. / Howard, R.J. / Malherbe, L. / Lee, U.S. / Corringer, P.J. / Harris, R.A. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hfc.cif.gz | 642.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hfc.ent.gz | 542.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hfc_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4hfc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4hfc_validation.xml.gz | 58.3 KB | Display | |
Data in CIF | 4hfc_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/4hfc ftp://data.pdbj.org/pub/pdb/validation_reports/hf/4hfc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | homo-pentamer |
-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36215.652 Da / Num. of mol.: 5 / Fragment: unp residues 44-359 / Mutation: F280A 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) / Strain (production host): BL21 C43 / References: UniProt: Q7NDN8 #2: Sugar | ChemComp-LMT / |
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-Non-polymers , 6 types, 122 molecules
#3: Chemical | ChemComp-BRJ / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-PLC / #7: Chemical | ChemComp-ACT / #8: 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: 5.18 Å3/Da / Density % sol: 76.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 12-15% PEG4K, 0.1M Na Acetate pH4, 0.4M NaSCN, 200 mM 2-bromo-ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9191 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2011 Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→49.6 Å / Num. obs: 70214 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 81.72 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.07 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.05→3.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10221 / Rsym value: 0.552 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.9044 / Cor.coef. Fo:Fc free: 0.8827 / SU R Cruickshank DPI: 0.493 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 86.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.566 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.13 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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