+Open data
-Basic information
Entry | Database: PDB / ID: 8jqy | ||||||
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Title | Crystal Structure of nucleotide-free mIRGB10 | ||||||
Components | Immunity-related GTPase family member b10 | ||||||
Keywords | IMMUNE SYSTEM / GTP hydrolase | ||||||
Function / homology | Function and homology information defense response to other organism / cellular response to interferon-beta / GTPase activity / endoplasmic reticulum membrane / GTP binding Similarity search - Function | ||||||
Biological species | Mus musculus molossinus (Japanese wild mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 Å | ||||||
Authors | Ha, H.J. / Park, H.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Front Immunol / Year: 2023 Title: Structural basis of IRGB10 oligomerization by GTP hydrolysis. Authors: Ha, H.J. / Kim, J.H. / Lee, G.H. / Kim, S. / Park, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jqy.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jqy.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 8jqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jqy_validation.pdf.gz | 428.4 KB | Display | wwPDB validaton report |
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Full document | 8jqy_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 8jqy_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 8jqy_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/8jqy ftp://data.pdbj.org/pub/pdb/validation_reports/jq/8jqy | HTTPS FTP |
-Related structure data
Related structure data | 8jqzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47119.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus molossinus (Japanese wild mouse) Gene: Irgb10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5NFV2 |
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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: 4.31 Å3/Da / Density % sol: 71.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, and 0.1 M Tris-HCl (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 3.68→29.61 Å / Num. obs: 8893 / % possible obs: 99.66 % / Redundancy: 20.7 % / Biso Wilson estimate: 138.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.54 |
Reflection shell | Resolution: 3.681→3.812 Å / Num. unique obs: 891 / CC1/2: 0.671 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.68→29.61 Å / SU ML: 0.5468 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3371 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 155.45 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.68→29.61 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: 66.3207665273 Å / Origin y: -60.7203405647 Å / Origin z: -16.2434791357 Å
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Refinement TLS group | Selection details: all |