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Yorodumi- PDB-1tq4: Crystal Structure of IIGP1: a paradigm for interferon inducible p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tq4 | ||||||
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Title | Crystal Structure of IIGP1: a paradigm for interferon inducible p47 resistance GTPases | ||||||
Components | interferon-inducible GTPase | ||||||
Keywords | SIGNALING PROTEIN / GTPase / Interferon gamma / dimer / immunology | ||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / autophagosome assembly / cellular response to interferon-beta / regulation of autophagy / response to bacterium / cytokine-mediated signaling pathway / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / autophagosome assembly / cellular response to interferon-beta / regulation of autophagy / response to bacterium / cytokine-mediated signaling pathway / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nuclear membrane / defense response to Gram-negative bacterium / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ghosh, A. / Uthaiah, R. / Howard, J. / Herrmann, C. / Wolf, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Crystal Structure of IIGP1; A Paradigm for Interferon-Inducible p47 Resistance GTPases Authors: Ghosh, A. / Uthaiah, R. / Howard, J. / Herrmann, C. / Wolf, E. #1: Journal: J.Biol.Chem. / Year: 2003 Title: IIGP1, an interferon-gamma-inducible 47-kDa GTPase of the mouse, showing cooperative enzymatic activity and GTP-dependent multimerization Authors: Uthaiah, R.C. / Praefcke, G.J.K. / Howard, J.C. / Herrmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tq4.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tq4.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tq4_validation.pdf.gz | 759.8 KB | Display | wwPDB validaton report |
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Full document | 1tq4_full_validation.pdf.gz | 766.7 KB | Display | |
Data in XML | 1tq4_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1tq4_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tq4 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tq4 | HTTPS FTP |
-Related 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: 47572.410 Da / Num. of mol.: 1 / Mutation: K48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: IIGP1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QZ85 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: 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: 2.5 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: PEG 4000, NaOAc, pH 4.6, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.986 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 17, 2004 |
Radiation | Monochromator: Sagital focusing double Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 31715 / Num. obs: 31715 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.049 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 7.9 / Rsym value: 0.264 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.95 Å / Rfactor Rfree error: 0.01
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