+Open data
-Basic information
Entry | Database: PDB / ID: 6ivk | ||||||
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Title | Crystal structure of a membrane protein G175A | ||||||
Components | Ibestrophin | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 | 6ivk.cif.gz | 280.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ivk.ent.gz | 227.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ivk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ivk_validation.pdf.gz | 515 KB | Display | wwPDB validaton report |
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Full document | 6ivk_full_validation.pdf.gz | 549.2 KB | Display | |
Data in XML | 6ivk_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 6ivk_validation.cif.gz | 70.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6ivk ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6ivk | HTTPS FTP |
-Related structure data
Related structure data | 6iv0C 6iv1C 6iv2C 6iv3C 6iv4C 6ivjC 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
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 33845.270 Da / Num. of mol.: 5 / Mutation: G175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) 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: Escherichia coli (E. coli) / References: UniProt: W9BH30, UniProt: W1ELP7*PLUS |
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-Non-polymers , 6 types, 157 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACY / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PGE / | #7: 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: 4.32 Å3/Da / Density % sol: 71.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.03 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-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→161.5 Å / Num. obs: 85727 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4527 / CC1/2: 0.765 / Rpim(I) all: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.64 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.71 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→48.64 Å
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Refine LS restraints |
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