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Yorodumi- PDB-5uzu: Immune evasion by a Staphylococcal Peroxidase Inhibitor that bloc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uzu | ||||||||||||
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Title | Immune evasion by a Staphylococcal Peroxidase Inhibitor that blocks myeloperoxidase | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / myeloperoxidase / phagolysosome / Staphylococcal inhibitor innate immunity | ||||||||||||
Function / homology | Function and homology information myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | ||||||||||||
Authors | de Jong, N. / Geisbrecht, B.V. / van Strijp, J. / Haas, P. / Nijland, R. / Ramyar, K. / Fevre, C. / Guerra, F. / Voyich-Kane, J. / van Kessel, C. / Garcia, B. | ||||||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Immune evasion by a staphylococcal inhibitor of myeloperoxidase. Authors: de Jong, N.W.M. / Ramyar, K.X. / Guerra, F.E. / Nijland, R. / Fevre, C. / Voyich, J.M. / McCarthy, A.J. / Garcia, B.L. / van Kessel, K.P.M. / van Strijp, J.A.G. / Geisbrecht, B.V. / Haas, P.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uzu.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uzu.ent.gz | 223 KB | Display | PDB format |
PDBx/mmJSON format | 5uzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uzu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5uzu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5uzu_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 5uzu_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/5uzu ftp://data.pdbj.org/pub/pdb/validation_reports/uz/5uzu | HTTPS FTP |
-Related structure data
Related structure data | 1cxpS S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules BA
#1: Protein | Mass: 7980.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: BN1321_100004, ERS072738_02531, ERS074020_02508, ERS140147_02483, HMPREF3211_00419 Production host: Escherichia coli (E. coli) / References: UniProt: W8TS31, UniProt: Q2G0X2*PLUS |
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#2: Protein | Mass: 65910.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPO / Cell line (production host): NS0 / Production host: Mus musculus (house mouse) / References: UniProt: P05164, myeloperoxidase |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 173 molecules
#6: Chemical | ChemComp-CA / | ||
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#7: Chemical | #8: 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: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG-3350 0.2M ammonium citrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 31978 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 39.79 Å2 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.056 / Rrim(I) all: 0.156 / Χ2: 1.016 / Net I/σ(I): 7 / Num. measured all: 240689 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXP Resolution: 2.403→43.342 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.43 / Stereochemistry target values: ML
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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: 2.403→43.342 Å
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Refine LS restraints |
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LS refinement shell |
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