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Yorodumi- PDB-6azp: A Structurally Dynamic N-terminal Region Drives Function of the S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6azp | |||||||||
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Title | A Structurally Dynamic N-terminal Region Drives Function of the Staphylococcal Peroxidase Inhibitor (SPIN) | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / myeloperoxidase / inhibitor / complex / innate immune evasion / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
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 / heme binding / chromatin binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å | |||||||||
Authors | Ramyar, K.X. / Geisbrecht, B.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (SPIN). Authors: de Jong, N.W.M. / Ploscariu, N.T. / Ramyar, K.X. / Garcia, B.L. / Herrera, A.I. / Prakash, O. / Katz, B.B. / Leidal, K.G. / Nauseef, W.M. / van Kessel, K.P.M. / van Strijp, J.A.G. / Geisbrecht, B.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6azp.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6azp.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 6azp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6azp ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azp | HTTPS FTP |
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-Related structure data
Related structure data | 5uzuS 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 AB
#1: Protein | Mass: 65839.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPO / Production host: Mus musculus (house mouse) / References: UniProt: P05164, myeloperoxidase |
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#2: Protein | Mass: 6922.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAMEA3448974_01858 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1K8H768, UniProt: Q2G0X2*PLUS |
-Sugars , 3 types, 4 molecules
#3: 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 | ||
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#4: Sugar | #5: Sugar | ChemComp-BMA / | |
-Non-polymers , 2 types, 283 molecules
#6: Chemical | ChemComp-CA / |
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#7: 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: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG3350, 0.2 M 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 225 mm CCD / Detector: CCD / Date: Dec 15, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.291→50 Å / Num. obs: 36486 / % possible obs: 99 % / Redundancy: 7.7 % / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5UZU Resolution: 2.291→38.958 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.43 Å2 / Biso mean: 42.0145 Å2 / Biso min: 13.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.291→38.958 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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