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Yorodumi- PDB-4rai: Crystal Structure of CNG mimicking NaK-ETPP mutant in complex with Na+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rai | ||||||
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Title | Crystal Structure of CNG mimicking NaK-ETPP mutant in complex with Na+ | ||||||
Components | Potassium channel protein | ||||||
Keywords | TRANSPORT PROTEIN / Alpha helical membrane protein / chimera channel | ||||||
Function / homology | Function and homology information stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | De March, M. / Napolitano, L.M.R. / Onesti, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. Authors: Napolitano, L.M. / Bisha, I. / De March, M. / Marchesi, A. / Arcangeletti, M. / Demitri, N. / Mazzolini, M. / Rodriguez, A. / Magistrato, A. / Onesti, S. / Laio, A. / Torre, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rai.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rai.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/4rai ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4rai | HTTPS FTP |
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-Related structure data
Related structure data | 4r50C 4r6zC 4r7cC 4r8cC 4ro2C 3k0dS 4r8b 4rar 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Tetrameric channel with pore on 4-fold axis |
-Components
#1: Protein | Mass: 10626.555 Da / Num. of mol.: 2 / Fragment: residues 20-110 / Mutation: D66E, G67T, N68P, F69P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_0669 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q81HW2 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-GLY / #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: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: CNG-ETPP(K+) crystals grown in 100mM MES pH 6.5, 60-66% (w/v) MPD, 100mM Glycine, Soaking O.N. in 70% MPD, 10mM DM, 100mM Hepes pH 7.5 and 100mM NaCl, VAPOR DIFFUSION, HANGING DROP PH range: 6.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→53.35 Å / Num. obs: 8580 / % possible obs: 99.3 % / Observed criterion σ(I): 1.7 |
Reflection shell | Resolution: 2.31→53.35 Å / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 5.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K0D Resolution: 2.31→53.35 Å / σ(F): 1.7 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.31→53.35 Å
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Refine LS restraints |
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