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Open data
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Basic information
Entry | Database: PDB / ID: 6b2d | |||||||||
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Title | Crystal structure of fluoride channel Fluc Ec2 T114S Mutant | |||||||||
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![]() | TRANSPORT PROTEIN / alpha helix / ion channel / membrane protein | |||||||||
Function / homology | ![]() fluoride channel activity / cellular detoxification of fluoride / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Last, N.B. / Sun, S. / Pham, M.C. / Miller, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular determinants of permeation in a fluoride-specific ion channel. Authors: Last, N.B. / Sun, S. / Pham, M.C. / Miller, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.6 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 945.5 KB | Display | ![]() |
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Full document | ![]() | 945.7 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b24C ![]() 6b2aC ![]() 6b2bC ![]() 5kbnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 13601.280 Da / Num. of mol.: 2 / Mutation: R25K, T114S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: crcB, A4T40_27000, AC789_145pl00540, AKG99_27195, BET08_05210, BK292_28205, BK334_22235, BK373_23795, BUE82_27975, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22 Plasmid: pET21 / Production host: ![]() ![]() #2: Protein | Mass: 10318.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 1 types, 3 molecules ![](data/chem/img/DMU.gif)
#4: Sugar |
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-Non-polymers , 3 types, 10 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.43 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 31% PEG 600, 100 mM ADA, 10 mM HEPES, 100 mM NaF, 50 mM LiNO3 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.01→37.84 Å / Num. obs: 21243 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.036 / Rrim(I) all: 0.106 / Net I/σ(I): 14.1 / Num. measured all: 185752 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KBN Resolution: 3.01→37.84 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.876 / SU B: 40.665 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.07 Å2 / Biso mean: 108.664 Å2 / Biso min: 81.44 Å2
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Refinement step | Cycle: final / Resolution: 3.01→37.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.01→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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