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Yorodumi- PDB-6iv4: Crystal structure of a bacterial Bestrophin homolog from Klebsiel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iv4 | ||||||
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Title | Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation W252F | ||||||
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: 3.14 Å | ||||||
Authors | Kittredge, A. / Chen, S. / Yang, T. | ||||||
Funding support | China, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iv4.cif.gz | 268.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iv4.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 6iv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iv4_validation.pdf.gz | 480.3 KB | Display | wwPDB validaton report |
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Full document | 6iv4_full_validation.pdf.gz | 517.5 KB | Display | |
Data in XML | 6iv4_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 6iv4_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6iv4 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6iv4 | HTTPS FTP |
-Related structure data
Related structure data | 6iv0C 6iv1C 6iv2C 6iv3C 6ivjC 6ivkC 6ivlC 6ivmC 6ivnC 6ivoC 6ivpC 6ivqC 6ivrC 6ivwC 6jlfC 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
#1: Protein | Mass: 33705.125 Da / Num. of mol.: 5 / Mutation: W252F 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 / |
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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: 3.85 Å3/Da / Density % sol: 68.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05M zinc acetate, 6% v/v ethylene glycol, 0.1M sodium cacodylate, pH 6.0, 6.6% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→61.93 Å / Num. obs: 45665 / % possible obs: 98.5 % / Redundancy: 3.4 % / Net I/σ(I): 8.77 |
Reflection shell | Resolution: 3.14→3.25 Å |
-Processing
Software |
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Refinement | Resolution: 3.14→61.93 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.14→61.93 Å
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Refine LS restraints |
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LS refinement shell |
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