+Open data
-Basic information
Entry | Database: PDB / ID: 1w6x | ||||||
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Title | SH3 domain of p40phox, component of the NADPH oxidase | ||||||
Components | NEUTROPHIL CYTOSOL FACTOR 4 | ||||||
Keywords | SH3 DOMAIN / NADPH OXIDASE / P40PHOX / PHAGOCYTE | ||||||
Function / homology | Function and homology information superoxide-generating NADPH oxidase activator activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / superoxide anion generation / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases ...superoxide-generating NADPH oxidase activator activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / superoxide anion generation / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC2 GTPase cycle / phagocytosis / RAC1 GTPase cycle / VEGFA-VEGFR2 Pathway / endosome membrane / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Massenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Effects of P47Phox C-Terminus Phosphorylation on Binding Interactions with P40Phox and P67Phox: Structural and Functional Comparison of P40Phox P67Phox SH3 Domains Authors: Massenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w6x.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w6x.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/1w6x ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w6x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6791.013 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 174-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHILE / Plasmid: PIVEX2.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15080 #2: Water | ChemComp-HOH / | Sequence details | THE STRUCTURE CORRESPOND | |
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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: 1.91 Å3/Da / Density % sol: 35.52 % Description: THE STARTING MODEL CONSISTED OF A SUPERPOSITION OF 8 SH3 STRUCTURES 1SEM, 1SHG, 1ABQ, 1FYN, 1I0C,1B07, 1BB9, 1BU1 USING MAIN CHAIN ATOMS |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion Details: VAPOR DIFFUSION AT 14 DEGRE C, PROTEIN AT 14 MG/ML, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 40% PEG2K MME, 100 MM AS 200 MM NA AC PH 4.6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: NONIUS / Wavelength: 1.54 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 6876 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9964 Å2 / ksol: 0.3542 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.93 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
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Xplor file |
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