+Open data
-Basic information
Entry | Database: PDB / ID: 6ivl | ||||||
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Title | Crystal structure of a membrane protein L259A | ||||||
Components | Ibestrophin | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / plasma membrane / ACETIC ACID / Ibestrophin / Ibestrophin Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Kittredge, A. / Fukuda, F. / Zhang, Y. / Yang, T. | ||||||
Funding support | United States, 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 | 6ivl.cif.gz | 274.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ivl.ent.gz | 222.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ivl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ivl_validation.pdf.gz | 492.4 KB | Display | wwPDB validaton report |
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Full document | 6ivl_full_validation.pdf.gz | 523.2 KB | Display | |
Data in XML | 6ivl_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 6ivl_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6ivl ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6ivl | HTTPS FTP |
-Related structure data
Related structure data | 6iv0C 6iv1C 6iv2C 6iv3C 6iv4C 6ivjC 6ivkC 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: 33789.164 Da / Num. of mol.: 5 / Mutation: L259A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U30_16350, B4U35_20780, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, D0897_06110, DXF97_13395, DY552_11160, DZB15_ ...Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U30_16350, B4U35_20780, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, D0897_06110, DXF97_13395, DY552_11160, DZB15_11820, NCTC11679_02573, NCTC13465_00112, NCTC5052_01714, NCTC8849_03195, NCTC9637_03467, NCTC9645_05950, NCTC9661_03571, SAMEA104305404_11875, SAMEA23986918_00256, SAMEA24002668_02597, SAMEA3649709_04169, SAMEA4394730_00268 Production host: Escherichia coli (E. coli) / References: UniProt: W9BH30, UniProt: W1ELP7*PLUS #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ACY / | #5: 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: 4.4 Å3/Da / Density % sol: 72.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.05 M zinc acetate, 6% v/v ethylene glycol, 0.1 M 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-C / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→161.9 Å / Num. obs: 41709 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.4→3.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4641 / CC1/2: 0.757 / Rpim(I) all: 0.345 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.8 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.86 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→48.8 Å
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Refine LS restraints |
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