[English] 日本語
Yorodumi- PDB-6jlf: Crystal structure of a bacterial Bestrophin homolog from Klebsiel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jlf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae D179A mutation - HR | ||||||
Components | Bestrophin homolog | ||||||
Keywords | MEMBRANE PROTEIN / Bestrophin-1 / homolog / mutation / klebsiella pneumoniae | ||||||
Function / homology | UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / Ibestrophin Function and homology information | ||||||
Biological species | Klebsiella pneumoniae IS53 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.548 Å | ||||||
Authors | Kittredge, A. / Chen, S. / Yang, T. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Dual Ca2+-dependent gates in human Bestrophin1 underlie disease-causing mechanisms of gain-of-function mutations. Authors: Ji, C. / Kittredge, A. / Hopiavuori, A. / Ward, N. / Chen, S. / Fukuda, Y. / Zhang, Y. / Yang, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jlf.cif.gz | 268.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jlf.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jlf_validation.pdf.gz | 482.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jlf_full_validation.pdf.gz | 520.5 KB | Display | |
Data in XML | 6jlf_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 6jlf_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/6jlf ftp://data.pdbj.org/pub/pdb/validation_reports/jl/6jlf | HTTPS FTP |
-Related structure data
Related structure data | 6iv0C 6iv1C 6iv2C 6iv3C 6iv4C 6ivjC 6ivkC 6ivlC 6ivmC 6ivnC 6ivoC 6ivpC 6ivqC 6ivrC 6ivwC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33787.230 Da / Num. of mol.: 5 / Mutation: D179A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae IS53 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1ELP7 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05M ZnAce, 6.6% PEG 8000, 0.1M Na-Cacodylat (pH 6.0), 6% EG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.548→93.195 Å / Num. obs: 95113 / % possible obs: 98.2 % / Redundancy: 3.4 % / Net I/σ(I): 18.74 |
Reflection shell | Resolution: 2.548→2.64 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.548→93.195 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.22
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.548→93.195 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|