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Yorodumi- PDB-2xq7: Pentameric ligand gated ion channel GLIC in complex with cadmium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xq7 | ||||||
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Title | Pentameric ligand gated ion channel GLIC in complex with cadmium ion (Cd2+) | ||||||
Components | GLR4197 PROTEIN | ||||||
Keywords | MEMBRANE PROTEIN / OPEN CHANNEL BLOCK | ||||||
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 7421 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.4 Å | ||||||
Authors | Hilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural Basis of Open Channel Block in a Prokaryotic Pentameric Ligand-Gated Ion Channel Authors: Hilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R. #1: Journal: Nature / Year: 2009 Title: Structure of a Potentially Open State of a Proton-Activated Pentameric Ligand-Gated Ion Channel. Authors: Hilf, R.J.C. / Dutzler, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xq7.cif.gz | 635 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xq7.ent.gz | 530.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xq7_validation.pdf.gz | 469.8 KB | Display | wwPDB validaton report |
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Full document | 2xq7_full_validation.pdf.gz | 561.6 KB | Display | |
Data in XML | 2xq7_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 2xq7_validation.cif.gz | 84.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/2xq7 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/2xq7 | HTTPS FTP |
-Related structure data
Related structure data | 2xq3C 2xq4C 2xq5C 2xq6C 2xq8C 2xq9C 2xqaC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: RESIDUES 43-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GLOEOBACTER VIOLACEUS PCC 7421 (bacteria) Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8 #2: Chemical | ChemComp-CD / |
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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: 5.16 Å3/Da / Density % sol: 76.2 % / Description: NONE |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 9% PEG 4000, 50MM CH3COONA, 200MM (NH4)2SO4, PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K, VAPOR DIFFUSION, HANGING DROP. |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 50052 / % possible obs: 87.1 % / Observed criterion σ(I): 3.1 / Redundancy: 3 % / Biso Wilson estimate: 93.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.4→40.2 Å / SU ML: 0.46 / σ(F): 1.89 / Phase error: 31.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.241 Å2 / ksol: 0.263 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.4→40.2 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.5775 Å / Origin y: 3.4938 Å / Origin z: 52.5921 Å
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Refinement TLS group | Selection details: ALL |