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Yorodumi- PDB-6bx4: The crystal structure of fluoride channel Fluc Ec2 with Monobody S9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bx4 | ||||||
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Title | The crystal structure of fluoride channel Fluc Ec2 with Monobody S9 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Fluc / Fluoride channel / monobody | ||||||
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: 2.55 Å | ||||||
Authors | Turman, D.L. / Miller, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Molecular Interactions between a Fluoride Ion Channel and Synthetic Protein Blockers. Authors: Turman, D.L. / Cheloff, A.Z. / Corrado, A.D. / Nathanson, J.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 | 6bx4.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bx4.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/6bx4 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/6bx4 | HTTPS FTP |
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-Related structure data
Related structure data | 6bx5C 5kbnS 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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2 |
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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: 13265.860 Da / Num. of mol.: 2 / Mutation: R25K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: crcB, A4T40_27000, A8M81_25235, AC789_145pl00540, AKG99_27195, B7C53_24430, BET08_05210, BIU72_24510, BK292_28205, BK334_22235, BK373_23795, BMR46_27175, BMR58_00505, BMR59_25090, BMR61_25795, ...Gene: crcB, A4T40_27000, A8M81_25235, AC789_145pl00540, AKG99_27195, B7C53_24430, BET08_05210, BIU72_24510, BK292_28205, BK334_22235, BK373_23795, BMR46_27175, BMR58_00505, BMR59_25090, BMR61_25795, CDL37_21115, CNQ53_00195, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22 Production host: Escherichia coli (E. coli) / References: UniProt: Q6J5N4 #2: Protein | Mass: 10318.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Engineered human fibronectin type III domain / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Sugars , 1 types, 2 molecules
#4: Sugar |
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-Non-polymers , 3 types, 126 molecules
#3: Chemical | ChemComp-F / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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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: 5.85 Å3/Da / Density % sol: 78.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM ADA-NaOH, 50 mM LiNO3, 31% PEG 600 / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.55→87.41 Å / Num. obs: 35318 / % possible obs: 99.9 % / Redundancy: 15.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.026 / Rrim(I) all: 0.102 / Net I/σ(I): 15.4 / Num. measured all: 533931 / Scaling rejects: 12832 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kbn Resolution: 2.55→84.34 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.2091 / FOM work R set: 0.8087 / SU B: 16.929 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2455 / SU Rfree: 0.2075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.208 / 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: 159.77 Å2 / Biso mean: 73.647 Å2 / Biso min: 47.1 Å2
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Refinement step | Cycle: final / Resolution: 2.55→84.34 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: 2.55→2.616 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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