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Yorodumi- PDB-5kum: Crystal Structure of Inward Rectifier Kir2.2 K62W Mutant In Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kum | ||||||
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Title | Crystal Structure of Inward Rectifier Kir2.2 K62W Mutant In Complex with PIP2 | ||||||
Components | ATP-sensitive inward rectifier potassium channel 12 | ||||||
Keywords | METAL TRANSPORT / Kir 2.2 K62W mutant structure | ||||||
Function / homology | Function and homology information Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lee, S.-J. / Ren, F. / Heyman, S. / Yuan, P. / Nichols, C.G. | ||||||
Citation | Journal: J.Gen.Physiol. / Year: 2016 Title: Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids. Authors: Lee, S.J. / Ren, F. / Zangerl-Plessl, E.M. / Heyman, S. / Stary-Weinzinger, A. / Yuan, P. / Nichols, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kum.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kum.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kum_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5kum_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5kum_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 5kum_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5kum ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5kum | HTTPS FTP |
-Related structure data
Related structure data | 5kukSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39418.754 Da / Num. of mol.: 1 / Fragment: UNP residues 38-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: KCNJ12 / Production host: Komagataella pastoris (fungus) / References: UniProt: F1NHE9 | ||||
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#2: Chemical | ChemComp-PIO / [( | ||||
#3: Chemical | ChemComp-K / #4: Sugar | ChemComp-DMU / | #5: Water | ChemComp-HOH / | |
-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: 293.15 K / Method: evaporation / Details: Hepes, KCl, PEG 400 / PH range: 6.3-6.8 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→91.95 Å / Num. obs: 14556 / % possible obs: 99.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.67 / CC1/2: 0.769 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KUK Resolution: 2.8→91.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.573 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 74.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→91.95 Å
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Refine LS restraints |
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