+Open data
-Basic information
Entry | Database: PDB / ID: 3piv | ||||||
---|---|---|---|---|---|---|---|
Title | Zebrafish interferon 1 | ||||||
Components | Interferon | ||||||
Keywords | CYTOKINE / Interferon / zebrafish | ||||||
Function / homology | Function and homology information : / : / type I interferon receptor binding / regulation of defense response to virus by host / response to arsenic-containing substance / response to exogenous dsRNA / cytokine activity / response to virus / defense response to virus / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.086 Å | ||||||
Authors | Hamming, O.J. / Hartmann, R. / Lutfalla, G. / Levraud, J.-P. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: Crystal Structure of Zebrafish Interferons I and II Reveals Conservation of Type I Interferon Structure in Vertebrates. Authors: Hamming, O.J. / Lutfalla, G. / Levraud, J.P. / Hartmann, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3piv.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3piv.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 3piv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3piv_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3piv_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 3piv_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3piv_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3piv ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3piv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19433.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ifnphi1, ifn1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AY12 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M NaCl, 20% PEG3350, 0.1 M HEPES pH 6.5, 3% (v/v) Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.8742 Å | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 | |||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8742 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.086→51.29 Å / Num. all: 17632 / Num. obs: 18309 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.4 | |||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.086→48.819 Å / SU ML: 0.26 / σ(F): 0.14 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.31 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.086→48.819 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|