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Yorodumi- PDB-6f1e: Crystal structure of olive flounder [Paralichthys olivaceus] inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f1e | |||||||||||||||
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Title | Crystal structure of olive flounder [Paralichthys olivaceus] interferon gamma at 2.3 Angstrom resolution | |||||||||||||||
Components | Interferon gamma | |||||||||||||||
Keywords | IMMUNE SYSTEM / Interferon gamma / Four-helix bundle / Antiviral defense | |||||||||||||||
Function / homology | Interferon gamma / type II interferon receptor binding / Four-helical cytokine-like, core / cytokine activity / immune response / protein homodimerization activity / extracellular space / Interferon gamma Function and homology information | |||||||||||||||
Biological species | Paralichthys olivaceus (Japanese flounder) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.296 Å | |||||||||||||||
Authors | Kolenko, P. / Kolarova, L. / Zahradnik, J. / Schneider, B. | |||||||||||||||
Funding support | Czech Republic, 4items
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Citation | Journal: Fish Shellfish Immunol. / Year: 2018 Title: Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function. Authors: Zahradnik, J. / Kolarova, L. / Parizkova, H. / Kolenko, P. / Schneider, B. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f1e.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1e.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 6f1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f1e_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 6f1e_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 6f1e_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 6f1e_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1e ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1e | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20431.641 Da / Num. of mol.: 2 / Mutation: Cdelta11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paralichthys olivaceus (Japanese flounder) Gene: Ifng / Plasmid: pET26bPoli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B3IXK1 #2: 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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein buffer: 100 mM citrate buffer, pH 6.0 Reservoir: 3 M NaCl 0.1 M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2017 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.296→49.6 Å / Num. obs: 20255 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Net I/σ(I): 13.5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.296→49.59 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 9.291 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 76.012 Å2
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Refinement step | Cycle: 1 / Resolution: 2.296→49.59 Å
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Refine LS restraints |
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