+Open data
-Basic information
Entry | Database: PDB / ID: 5kom | ||||||
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Title | The crystal structure of fluoride channel Fluc Ec2 F83I Mutant | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / alpha helix / ion channel / membrane protein | ||||||
Function / homology | Function and homology information fluoride channel activity / cellular detoxification of fluoride / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.69 Å | ||||||
Authors | Last, N.B. / Kolmakova-Partensky, L. / Shane, T. / Miller, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2016 Title: Mechanistic signs of double-barreled structure in a fluoride ion channel. Authors: Last, N.B. / Kolmakova-Partensky, L. / Shane, T. / Miller, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kom.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kom.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/5kom ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5kom | HTTPS FTP |
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-Related structure data
Related structure data | 5kbnC 5a43S S: Starting model for refinement 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 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: 15808.770 Da / Num. of mol.: 2 / Mutation: R25K, F83I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: crcB, AC789_145pl00540, AKG99_27195, AL505_410006, AN206_26275, AUQ25_20445, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22, SK78_04822 Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6J5N4 #2: Protein | Mass: 10375.529 Da / Num. of mol.: 2 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) |
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-Sugars , 1 types, 3 molecules
#4: Sugar |
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-Non-polymers , 3 types, 12 molecules
#3: Chemical | ChemComp-NA / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.28 Å3/Da / Density % sol: 76.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 36% 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2015 | |||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.69→38.01 Å / Num. obs: 30195 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A43 Resolution: 2.69→38.01 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.909 / SU B: 21.365 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.218 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.63 Å2 / Biso mean: 75.044 Å2 / Biso min: 52.55 Å2
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Refinement step | Cycle: final / Resolution: 2.69→38.01 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: 2.69→2.76 Å / 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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