+Open data
-Basic information
Entry | Database: PDB / ID: 7wkh | ||||||
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Title | the grass carp IFNa | ||||||
Components | Interferon | ||||||
Keywords | CYTOKINE / fish / interferon | ||||||
Function / homology | Interferon beta / type I interferon receptor binding / Interferon alpha/beta/delta / Interferon alpha/beta domain / Four-helical cytokine-like, core / cytokine activity / defense response to virus / extracellular region / Interferon Function and homology information | ||||||
Biological species | Ctenopharyngodon idella (grass carp) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Zou, J. / WANG, J. / Wang, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Immunol / Year: 2022 Title: Structural and Functional Analyses of Type I IFNa Shed Light Into Its Interaction With Multiple Receptors in Fish. Authors: Wang, Z. / Xu, J. / Feng, J. / Wu, K. / Chen, K. / Jia, Z. / Zhu, X. / Huang, W. / Zhao, X. / Liu, Q. / Wang, B. / Chen, X. / Wang, J. / Zou, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wkh.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wkh.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wkh_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 7wkh_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 7wkh_validation.xml.gz | 10 KB | Display | |
Data in CIF | 7wkh_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/7wkh ftp://data.pdbj.org/pub/pdb/validation_reports/wk/7wkh | HTTPS FTP |
-Related structure data
Related structure data | 3pivS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19051.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: IFN / Production host: Escherichia coli (E. coli) / References: UniProt: Q2HZY8 |
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#2: 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: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 20%(W/V) PEG 3350, 200 mM Ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 28576 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.971 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 1.58→4.29 Å / Num. unique obs: 21056 / CC1/2: 0.971 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3piv Resolution: 1.58→27.755 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.102 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.245 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→27.755 Å
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LS refinement shell |
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