+Open data
-Basic information
Entry | Database: PDB / ID: 4x37 | ||||||
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Title | Gallus interleukin-1 mutant - E118K | ||||||
Components | IL-1 beta | ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information chemokine production / Interleukin-38 signaling / Interleukin-37 signaling / : / Interleukin-1 signaling / cortisol secretion / leukocyte activation involved in inflammatory response / leukocyte chemotaxis involved in inflammatory response / detection of lipopolysaccharide / sexual reproduction ...chemokine production / Interleukin-38 signaling / Interleukin-37 signaling / : / Interleukin-1 signaling / cortisol secretion / leukocyte activation involved in inflammatory response / leukocyte chemotaxis involved in inflammatory response / detection of lipopolysaccharide / sexual reproduction / fever generation / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / cellular response to cold / toll-like receptor signaling pathway / cytokine activity / acute-phase response / response to virus / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to lipopolysaccharide / inflammatory response / positive regulation of gene expression / extracellular space Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Yin, H.S. / Cheng, W.T. / Cheng, T. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To Be Published Title: Gallus interleukin-1 mutant - E118K Authors: Yin, H.S. / Cheng, W.T. / Cheng, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x37.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x37.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x37 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x37 | HTTPS FTP |
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-Related structure data
Related structure data | 2wryS 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
#1: Protein | Mass: 18904.533 Da / Num. of mol.: 1 / Mutation: E118K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: il-1beta, IL1B, IL1beta / Production host: Escherichia coli (E. coli) / References: UniProt: O73909 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.15 M (NH4)2SO4, 0.1 M Tris, 0.2 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→29.2 Å / Num. obs: 17881 / % possible obs: 98.7 % / Redundancy: 8.8 % / Net I/σ(I): 66.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WRY Resolution: 1.63→29.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.006 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.218 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→29.2 Å
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Refine LS restraints |
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