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Yorodumi- PDB-1hh8: The active N-terminal region of p67phox: Structure at 1.8 Angstro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hh8 | ||||||
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Title | The active N-terminal region of p67phox: Structure at 1.8 Angstrom resolution and biochemical characterizations of the A128V mutant implicated in chronic granulomatous disease | ||||||
Components | NEUTROPHIL CYTOSOL FACTOR 2 | ||||||
Keywords | CELL CYCLE / PHAGOCYTE OXIDASE FACTOR / SH3 DOMAIN / TPR REPEAT CELL CYCLE | ||||||
Function / homology | Function and homology information superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / superoxide anion generation / superoxide metabolic process / Detoxification of Reactive Oxygen Species ...superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / superoxide anion generation / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC2 GTPase cycle / cellular defense response / phagocytosis / RAC1 GTPase cycle / acrosomal vesicle / small GTPase binding / VEGFA-VEGFR2 Pathway / electron transfer activity / innate immune response / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Grizot, S. / Fieschi, F. / Dagher, M.-C. / Pebay-Peyroula, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The Active N-Terminal Region of P67Phox: Structure at 1.8 Angstrom Resolution and Biochemical Characterizations of the A128V Mutant Implicated in Chronic Granulomatous Disease Authors: Grizot, S. / Fieschi, F. / Dagher, M.-C. / Pebay-Peyroula, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hh8.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hh8.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hh8 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hh8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24518.551 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHIL / Cellular location: CYTOPLASM / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19878 |
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#2: Chemical | ChemComp-FLC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 45 % Description: PHASES AT 2.8 A WERE OBTAINED FROM A SAD DATA SET COLLECTED ON ID29 USING A SE-MET PROTEIN | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 100 MM NA CITRATE PH 4.5, 17% PEG 2K MME, 10% GLYCEROL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Date: Oct 15, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 23850 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.047 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.198 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 95808 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 972845 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8284 Å2 / ksol: 0.370973 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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