+Open data
-Basic information
Entry | Database: PDB / ID: 7ves | ||||||||||||||||||||||||||||||||||||
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Title | Crystal Structure of nucleotide-free Irgb6 | ||||||||||||||||||||||||||||||||||||
Components | T-cell-specific guanine nucleotide triphosphate-binding protein 2 | ||||||||||||||||||||||||||||||||||||
Keywords | HYDROLASE / Irgb6 / IRGs / immunity-related GTPase / (IFN)-inducible GTPase / p47 GTPase / tgtp / dynamin superfamily / IMMUNE SYSTEM | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information defense response to protozoan / cellular response to interferon-beta / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||||||||||||||||||||||||||
Authors | Saijo-Hamano, Y. / Sakai, N. / Nitta, R. | ||||||||||||||||||||||||||||||||||||
Funding support | Japan, 11items
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Citation | Journal: Life Sci Alliance / Year: 2022 Title: Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6. Authors: Saijo-Hamano, Y. / Sherif, A.A. / Pradipta, A. / Sasai, M. / Sakai, N. / Sakihama, Y. / Yamamoto, M. / Standley, D.M. / Nitta, R. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ves.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ves.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ves.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/7ves ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7ves | HTTPS FTP |
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-Related structure data
Related structure data | 7vexC 1tpzS 1tq2S 1tqdS S: Starting model for refinement C: citing same article (ref.) |
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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: 47330.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgtp2, Ifggb6, Irgb6, Mg21, Tgtp / Production host: Escherichia coli (E. coli) References: UniProt: Q3T9E4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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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: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: MIB buffer, Polyethylene Glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→40.13 Å / Num. obs: 61062 / % possible obs: 96.5 % / Redundancy: 4.62 % / Biso Wilson estimate: 35.74 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.63 |
Reflection shell | Resolution: 1.89→2 Å / Num. unique obs: 8033 / CC1/2: 0.422 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TQD, 1TPZ, 1TQ2 Resolution: 2→40.13 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1648 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: 42.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.13 Å
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Refine LS restraints |
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LS refinement shell |
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