+Open data
-Basic information
Entry | Database: PDB / ID: 8idx | ||||||
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Title | Structure of p205 HIN | ||||||
Components | Interferon-activable protein 205-B | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information cellular response to interferon-beta / activation of innate immune response / Neutrophil degranulation / nuclear periphery / double-stranded DNA binding / nuclear speck / nucleolus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Li, Y.L. / Jin, T.C. | ||||||
Funding support | 1items
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Citation | Journal: to Be published Title: Structure of p205 HIN Authors: Li, Y.L. / Jin, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8idx.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8idx.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 8idx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/8idx ftp://data.pdbj.org/pub/pdb/validation_reports/id/8idx | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24553.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mnda, Ifi205b / Plasmid: PET30a / Details (production host): MBP tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DOV1 #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 25% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→29.546 Å / Num. obs: 158200 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.02271 / Rpim(I) all: 0.01421 / Rrim(I) all: 0.02688 / Net I/σ(I): 28.96 |
Reflection shell | Resolution: 1.75→1.813 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2504 / Num. unique obs: 15198 / CC1/2: 0.969 / CC star: 0.992 / Rrim(I) all: 0.2991 / % possible all: 94.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.546 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→29.546 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.2558 Å / Origin y: -7.9458 Å / Origin z: 9.4848 Å
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Refinement TLS group | Selection details: all |