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Open data
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Basic information
Entry | Database: PDB / ID: 6ivm | ||||||
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Title | Crystal structure of a membrane protein P143A | ||||||
![]() | Ibestrophin | ||||||
![]() | MEMBRANE PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kittredge, A. / Fukuda, F. / Zhang, Y. / Yang, T. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.8 KB | Display | ![]() |
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PDB format | ![]() | 226.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.6 KB | Display | ![]() |
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Full document | ![]() | 532.9 KB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 65.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iv0C ![]() 6iv1C ![]() 6iv2C ![]() 6iv3C ![]() 6iv4C ![]() 6ivjC ![]() 6ivkC ![]() 6ivlC ![]() 6ivnC ![]() 6ivoC ![]() 6ivpC ![]() 6ivqC ![]() 6ivrC ![]() 6ivwC ![]() 6jlfC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 33805.203 Da / Num. of mol.: 5 / Mutation: P143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U27_02655, B4U30_16350, B4U35_20780, BB785_13310, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, CWQ24_13475, DM060_ ...Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U27_02655, B4U30_16350, B4U35_20780, BB785_13310, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, CWQ24_13475, DM060_34770, DM071_16710, DM078_14870, DM083_28480, DMR37_19630, DXF97_13395, NCTC11679_02573, NCTC13465_00112, NCTC5052_01714, NCTC8849_03195, NCTC9637_03467, NCTC9645_05950, NCTC9661_03571, SAMEA104305404_11875, SAMEA23986918_00256, SAMEA24002668_02597, SAMEA24012418_00268, SAMEA3649709_04169, SAMEA3673019_02937, SAMEA3727643_02313, SAMEA4394730_00268 Production host: ![]() ![]() |
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-Non-polymers , 8 types, 114 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/LEU.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/LEU.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-LEU / | #6: Chemical | #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / 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: ![]() ![]() ![]() |
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: 2.95→158.82 Å / Num. obs: 60739 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.083 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.907 / Num. unique obs: 4465 / CC1/2: 0.666 / Rpim(I) all: 0.54 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.888 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→48.72 Å
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Refine LS restraints |
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