+Open data
-Basic information
Entry | Database: PDB / ID: 5a40 | ||||||
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Title | Crystal structure of a dual topology fluoride ion channel. | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / FLUORIDE ION CHANNEL / MONOBODY / BPE | ||||||
Function / homology | Function and homology information fluoride channel activity / cellular detoxification of fluoride / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | BORDETELLA PERTUSSIS (bacteria) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å | ||||||
Authors | Stockbridge, R.B. / Kolmakova-Partensky, L. / Shane, T. / Koide, A. / Koide, S. / Miller, C. / Newstead, S. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Crystal Structures of a Double-Barrelled Fluoride Ion Channel. Authors: Stockbridge, R.B. / Kolmakova-Partensky, L. / Shane, T. / Koide, A. / Koide, S. / Miller, C. / Newstead, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a40.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a40.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 5a40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a40_validation.pdf.gz | 482.1 KB | Display | wwPDB validaton report |
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Full document | 5a40_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 5a40_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 5a40_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a40 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a40 | HTTPS FTP |
-Related structure data
Related structure data | 5a43C 5nkqC 5a41 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13291.635 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BORDETELLA PERTUSSIS (bacteria) / Strain: TOHAMA 1 / Plasmid: PASK-IBA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VYU0 #2: Protein | Mass: 10035.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHFT2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #3: Chemical | ChemComp-HG / |
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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: 5.39 Å3/Da / Density % sol: 77 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 36-41% PEG 550 MME, 0.2M MGCL, 0.1M TRIS-HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.006 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48 Å / Num. obs: 23518 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 83.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.6→3.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.6→114.708 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.846 / SU B: 25.286 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.73 / ESU R Free: 0.56 / 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 / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.589 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→114.708 Å
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Refine LS restraints |
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