+Open data
-Basic information
Entry | Database: PDB / ID: 6bqo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a dual topology fluoride channel with monobody S8 | |||||||||
Components |
| |||||||||
Keywords | MEMBRANE PROTEIN / Fluoride channel / monobody / dual topology | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Stockbridge, R.B. / Newstead, S. / McIlwain, B.C. | |||||||||
Funding support | United States, United Kingdom, 2items
| |||||||||
Citation | Journal: Structure / Year: 2018 Title: Cork-in-Bottle Occlusion of Fluoride Ion Channels by Crystallization Chaperones. Authors: McIlwain, B.C. / Newstead, S. / Stockbridge, R.B. #1: Journal: To Be Published Title: Structure of fluoride ion channel Fluc-Bpe in complex with monobody S8 Authors: McIlwain, B.C. / Newstead, S. / Stockbridge, R.B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6bqo.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bqo.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bqo_validation.pdf.gz | 808.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6bqo_full_validation.pdf.gz | 805.9 KB | Display | |
Data in XML | 6bqo_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6bqo_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/6bqo ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bqo | HTTPS FTP |
-Related structure data
Related structure data | 5nkqS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 13291.635 Da / Num. of mol.: 2 / Mutation: E94C, R29K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria) Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: crcB, BP1217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7VYU0 #2: Protein | | Mass: 10383.466 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
---|
-Non-polymers , 4 types, 53 molecules
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: 26% PEG 550MME, 0.1M sodium citrate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→27.969 Å / Num. obs: 11986 / % possible obs: 99.56 % / Redundancy: 8.3 % / Net I/σ(I): 11.68 |
Reflection shell | Resolution: 2.8→2.9 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NKQ Resolution: 2.8→27.969 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.14
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→27.969 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|