+Open data
-Basic information
Entry | Database: PDB / ID: 6dz1 | ||||||
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Title | Studies of Ion Transport in K+ Channels | ||||||
Components | Potassium channel protein | ||||||
Keywords | MEMBRANE PROTEIN / K ion transport channel | ||||||
Function / homology | Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / membrane => GO:0016020 / Orthogonal Bundle / Mainly Alpha / : / Potassium channel protein Function and homology information | ||||||
Biological species | Bacillus cereus BDRD-Cer4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å | ||||||
Authors | Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Wagner, A. / Duman, R. / El Omari, K. / Afonine, P.V. / Coates, L. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Anomalous X-ray diffraction studies of ion transport in K+channels. Authors: Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Afonine, P.V. / El Omari, K. / Duman, R. / Wagner, A. / Coates, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dz1.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dz1.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 6dz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/6dz1 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/6dz1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 10569.399 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus BDRD-Cer4 (bacteria) / Gene: bcere0015_5640 / Production host: Escherichia coli (E. coli) / References: UniProt: C2SWC7 #2: Chemical | ChemComp-K / #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: 2.45 Å3/Da / Density % sol: 49.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: Prepared by mixing equal volumes of protein solution in buffer (20mM Tris:HCl pH 7.8, 100mM KCl, and 4mM Anagrade DM) with well solution (72.5%MPD, 100mM KCl, and 100mM MES pH 6) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.35 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.35 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→54.15 Å / Num. obs: 18417 / % possible obs: 97.8 % / Redundancy: 8.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.019 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2.26→2.33 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 10.7 / CC1/2: 0.987 / Rpim(I) all: 0.082 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.26→54.154 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 21.61 / 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: 2.26→54.154 Å
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Refine LS restraints |
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LS refinement shell |
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