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Yorodumi- PDB-2b92: Crystal-structure of the N-terminal Large GTPase Domain of human ... -
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-Basic information
Entry | Database: PDB / ID: 2b92 | ||||||
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Title | Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GDP/AlF3 | ||||||
Components | Interferon-induced guanylate-binding protein 1 | ||||||
Keywords | SIGNALING PROTEIN / protein- guanine nucleotide complex | ||||||
Function / homology | Function and homology information GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptosis / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptosis / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Ghosh, A. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C. | ||||||
Citation | Journal: Nature / Year: 2006 Title: How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Authors: Ghosh, A. / Praefcke, G.J. / Renault, L. / Wittinghofer, A. / Herrmann, C. #1: Journal: Embo J. / Year: 2000 Title: Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism. Authors: Prakash, B. / Renault, L. / Praefcke, G.J. / Herrmann, C. / Wittinghofer, A. #2: Journal: Nature / Year: 2000 Title: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. Authors: Prakash, B. / Praefcke, G.J. / Renault, L. / Herrmann, C. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b92.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b92.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 2b92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/2b92 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/2b92 | HTTPS FTP |
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-Related structure data
Related structure data | 2b8wSC 2bc9C 2d4hC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Details | The biological assembly is the homodimer in the asymmetric unit |
-Components
#1: Protein | Mass: 37078.449 Da / Num. of mol.: 2 / Fragment: N-terminal Large GTPase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32455 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.14 Å3/Da / Density % sol: 60.78 % |
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Crystal grow | Temperature: 298 K Details: 12.5% Peg3350, 125mM Na2HPO4 (from Hampton Research peg/ion screen supplied at pH9.1), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002 / Details: GE(220) CRYSTAL |
Radiation | Monochromator: DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 14438 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 90.1 Å2 / Rsym value: 0.092 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.457 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B8W Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 41.573 / SU ML: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.57 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.26 Å / Total num. of bins used: 27
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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