+Open data
-Basic information
Entry | Database: PDB / ID: 6vhi | ||||||
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Title | Crystal structure of the human ILRUN Fw domain | ||||||
Components | Protein ILRUN | ||||||
Keywords | IMMUNE SYSTEM / Fw domain / innate immune system / immunoglobulin fold | ||||||
Function / homology | Function and homology information negative regulation of defense response to virus / phagophore assembly site / negative regulation of protein localization to nucleus / negative regulation of type I interferon production / negative regulation of DNA binding / negative regulation of tumor necrosis factor production / ubiquitin binding / macroautophagy / innate immune response / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Caputo, A.T. / Adams, T.E. | ||||||
Citation | Journal: Heliyon / Year: 2020 Title: Molecular characterisation of ILRUN, a novel inhibitor of proinflammatory and antimicrobial cytokines. Authors: Ambrose, R.L. / Brice, A.M. / Caputo, A.T. / Alexander, M.R. / Tribolet, L. / Liu, Y.C. / Adams, T.E. / Bean, A.G.D. / Stewart, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vhi.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vhi.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vhi_validation.pdf.gz | 247.6 KB | Display | wwPDB validaton report |
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Full document | 6vhi_full_validation.pdf.gz | 247.6 KB | Display | |
Data in XML | 6vhi_validation.xml.gz | 949 B | Display | |
Data in CIF | 6vhi_validation.cif.gz | 2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhi ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhi | HTTPS FTP |
-Related structure data
Related structure data | 4oleS 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: 13384.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ILRUN, C6orf106 / Plasmid: pET43 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6K1 |
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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: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1 M ammonium sulfate and 0.15 M trisodium citrate-citric acid, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45865 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45865 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→67.94 Å / Num. obs: 4775 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.061 / Rrim(I) all: 0.134 / Χ2: 0.79 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.46→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 709 / CC1/2: 0.89 / Rpim(I) all: 0.306 / Rrim(I) all: 0.658 / Χ2: 0.62 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OLE Resolution: 2.46→67.94 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.352 / SU Rfree Blow DPI: 0.223 / Details: used LSSR restraints generated from PDB entry 4OLE
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Displacement parameters | Biso mean: 57.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→67.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.54 Å
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Refinement TLS params. | Origin x: 23.6769 Å / Origin y: 14.4436 Å / Origin z: 5.7397 Å
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Refinement TLS group | Selection details: { A|* } |