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Yorodumi- PDB-7oih: Glycosylation in the crystal structure of neutrophil myeloperoxidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oih | ||||||
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Title | Glycosylation in the crystal structure of neutrophil myeloperoxidase | ||||||
Components | Myeloperoxidase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Peroxidase / microbicidal / hypochlorous acid / glycosylation / paucimannose / hydrid N-glycan / polymorphonuclear leukocytes / dimer | ||||||
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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å | ||||||
Authors | Krawczyk, L. / Semwal, S. / Bouckaert, J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase. Authors: Krawczyk, L. / Semwal, S. / Soubhye, J. / Lemri Ouadriri, S. / Prevost, M. / Van Antwerpen, P. / Roos, G. / Bouckaert, J. #1: Journal: J.Biol.Chem. / Year: 2010 Title: Glycosylation pattern of mature dimeric leukocyte and recombinant monomeric myeloperoxidase: glycosylation is required for optimal enzymatic activity Authors: Van Antwerpen, P. / Slomianny, M.-C. / Zouaoui Boudjeltia, K. / Delporte, C. / Faid, V. / Calay, D. / Rousseau, A. / Moguilevsky, N. / Raes, M. / Vanhamme, L. / Furtmuller, P.G. / Obinger, C. ...Authors: Van Antwerpen, P. / Slomianny, M.-C. / Zouaoui Boudjeltia, K. / Delporte, C. / Faid, V. / Calay, D. / Rousseau, A. / Moguilevsky, N. / Raes, M. / Vanhamme, L. / Furtmuller, P.G. / Obinger, C. / Vanhaeverbeek, M. / Neve, J. / Michalski, J.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oih.cif.gz | 1007 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oih.ent.gz | 841.6 KB | Display | PDB format |
PDBx/mmJSON format | 7oih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oih_validation.pdf.gz | 13.9 MB | Display | wwPDB validaton report |
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Full document | 7oih_full_validation.pdf.gz | 14 MB | Display | |
Data in XML | 7oih_validation.xml.gz | 199.9 KB | Display | |
Data in CIF | 7oih_validation.cif.gz | 280.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/7oih ftp://data.pdbj.org/pub/pdb/validation_reports/oi/7oih | HTTPS FTP |
-Related structure data
Related structure data | 6bmtS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 66011.492 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase |
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-Sugars , 9 types, 30 molecules
#2: 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 #3: Polysaccharide | Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #16: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 2508 molecules
#10: Chemical | ChemComp-CL / #11: Chemical | ChemComp-CA / #12: Chemical | ChemComp-HEM / #13: Chemical | ChemComp-SCN / #14: Chemical | ChemComp-8PR / #15: Chemical | ChemComp-PO4 / #17: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.55 Å3/Da / Density % sol: 51.85 % / Description: Bipyramidal tetrahedral |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Potassium thiocyanate 0.1 M Sodium cacodylate 8% w/v PGA L/M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 158296 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 54.98 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.195 / Net I/σ(I): 7.47 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 3.45 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 24289 / CC1/2: 0.409 / Rrim(I) all: 1.47 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BMT Resolution: 2.603→38.994 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.156 / SU B: 0.001 / SU ML: 0 / Average fsc free: 0.9541 / Average fsc work: 0.9679 / Cross valid method: FREE R-VALUE / ESU R: 0.241 / ESU R Free: 0.295 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.008 Å2
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Refinement step | Cycle: LAST / Resolution: 2.603→38.994 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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