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Open data
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Basic information
Entry | Database: PDB / ID: 6b2b | |||||||||
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Title | Crystal structure of fluoride channel Fluc Ec2 F83M Mutant | |||||||||
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Function / homology | ![]() fluoride channel activity / cellular detoxification of fluoride / ![]() ![]() 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 | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6b24C ![]() 6b2aC ![]() 6b2dC ![]() 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: 0 / Refine code: 0
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 13599.328 Da / Num. of mol.: 2 / Mutation: R25K, F83M 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)
#3: Sugar |
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-Non-polymers , 3 types, 19 molecules ![](data/chem/img/F.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ![]() #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.59 Å3/Da / Density % sol: 78.01 % / Mosaicity: 0.26 ° |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion / pH: 6 Details: 30% PEG 550mme, 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: May 18, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→47.14 Å / Num. obs: 32347 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Net I/σ(I): 15 / Num. measured all: 415917 / 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: 2.6→47.14 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 22.562 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.222 / 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: 149.69 Å2 / Biso mean: 82.65 Å2 / Biso min: 56.45 Å2
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Refinement step | Cycle: final / Resolution: 2.6→47.14 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: 2.6→2.667 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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