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Yorodumi- PDB-5fph: The GTPase domains of the immunity-related Irga6 dimerize in a pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fph | |||||||||
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Title | The GTPase domains of the immunity-related Irga6 dimerize in a parallel head-to-head fashion | |||||||||
Components | INTERFERON-INDUCIBLE GTPASE 1 | |||||||||
Keywords | HYDROLASE / IRGA6 / GMPPNP / INNATE IMMUNITY / IRG PROTEINS / GTPASE / DYNAMIN SUPERFAMILY / OLIGOMERIZATION | |||||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / innate immune response / GTPase activity / GTP binding / endoplasmic reticulum membrane / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Schulte, K. / Pawlowski, N. / Faelber, K. / Froehlich, C. / Howard, J. / Daumke, O. | |||||||||
Citation | Journal: Bmc Biol. / Year: 2016 Title: The Immunity-Related Gtpase Irga6 Dimerizes in a Parallel Head-to-Head Fashion. Authors: Schulte, K. / Pawlowski, N. / Faelber, K. / Froehlich, C. / Howard, J. / Daumke, O. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fph.cif.gz | 564.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fph.ent.gz | 467.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fph ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fph | HTTPS FTP |
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-Related structure data
Related structure data | 1tq2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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6 |
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7 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 48972.047 Da / Num. of mol.: 7 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 References: UniProt: Q9QZ85, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Details: 33% PEG 4000 3 % ISOPROPANOL 50 MM HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.972 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012 / Details: 3 SILICON MIRRORS |
Radiation | Monochromator: SILICON DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→214.9 Å / Num. obs: 115430 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 15.82 % / Biso Wilson estimate: 75.35 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.74 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TQ2 Resolution: 3.2→68.978 Å / SU ML: 0.63 / σ(F): 1.36 / Phase error: 31.79 / Stereochemistry target values: ML Details: FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-14, 200-202, 357 CHAIN B 1-14, 356-357 CHAIN C 1-14, 195-199, 333-334, 355-357 CHAIN D 1-13, 197-200 CHAIN E 1-13, 197-199, 356 CHAIN F 1-12, 105- ...Details: FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-14, 200-202, 357 CHAIN B 1-14, 356-357 CHAIN C 1-14, 195-199, 333-334, 355-357 CHAIN D 1-13, 197-200 CHAIN E 1-13, 197-199, 356 CHAIN F 1-12, 105-106, 196-198, 298, 356-357 CHAIN G 413
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→68.978 Å
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Refine LS restraints |
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LS refinement shell |
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