+Open data
-Basic information
Entry | Database: PDB / ID: 4pdm | ||||||||||||
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Title | Crystal Structure of K+ selective NaK mutant in rubidium | ||||||||||||
Components | Potassium channel protein | ||||||||||||
Keywords | TRANSPORT PROTEIN / Bacillus cereus / Binding Sites / Electrophysiology / Ions / Potassium / Potassium Channels / Sodium / rubidium / blockage | ||||||||||||
Function / homology | Function and homology information potassium channel activity / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Bacillus cereus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||||||||
Authors | Lam, Y. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: High Resolution Structural Views of Rubidium, Cesium and Barium Binding within a Potassium Selective Channel Filter Authors: Lam, Y. / Zeng, W. / Sauer, D.B. / Jiang, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pdm.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pdm.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/4pdm ftp://data.pdbj.org/pub/pdb/validation_reports/pd/4pdm | HTTPS FTP |
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-Related structure data
Related structure data | 4pdlC 4pdrC 4pdvC 3oufS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 10771.673 Da / Num. of mol.: 2 / Fragment: UNP residues 20-110 / Mutation: D66Y,N68D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q81HW2 #2: Chemical | ChemComp-RB / #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 65%MPD, 100mM KCl, 100mM MES, 4mM n-Decyl-beta-D-Maltoside PH range: 6.0-7.5 |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 27782 / % possible obs: 99.86 % / Redundancy: 7.4 % / Rsym value: 0.049 / Net I/σ(I): 48.3 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OUF Resolution: 1.58→34.005 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→34.005 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.2467 Å / Origin y: -9.458 Å / Origin z: 0.5023 Å
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Refinement TLS group | Selection details: all |