+Open data
-Basic information
Entry | Database: PDB / ID: 4ejx | |||||||||
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Title | Structure of ceruloplasmin-myeloperoxidase complex | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / cupredoxin domains / glycoproteins / protein-protein interaction | |||||||||
Function / homology | Function and homology information glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor ...glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / glutathione peroxidase / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / copper ion transport / respiratory burst involved in defense response / glutathione peroxidase activity / low-density lipoprotein particle remodeling / response to food / azurophil granule / ferroxidase / intracellular copper ion homeostasis / ferroxidase activity / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / Post-translational protein phosphorylation / Iron uptake and transport / peroxidase activity / defense response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / azurophil granule lumen / heparin binding / protein-folding chaperone binding / iron ion transport / intracellular iron ion homeostasis / response to oxidative stress / response to lipopolysaccharide / blood microparticle / oxidoreductase activity / lysosome / defense response to bacterium / copper ion binding / endoplasmic reticulum lumen / lysosomal membrane / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.69 Å | |||||||||
Authors | Samygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Vasilyev, V.B. / Bartunik, H. | |||||||||
Citation | Journal: Plos One / Year: 2013 Title: Ceruloplasmin: macromolecular assemblies with iron-containing acute phase proteins. Authors: Samygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Petoukhov, M.V. / Pulina, M.O. / Zakharova, E.T. / Vasilyev, V.B. / Bartunik, H. / Svergun, D.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ejx.cif.gz | 303.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ejx.ent.gz | 231.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ejx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ejx_validation.pdf.gz | 961.1 KB | Display | wwPDB validaton report |
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Full document | 4ejx_full_validation.pdf.gz | 1004.7 KB | Display | |
Data in XML | 4ejx_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 4ejx_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/4ejx ftp://data.pdbj.org/pub/pdb/validation_reports/ej/4ejx | HTTPS FTP |
-Related structure data
Related structure data | 4enzC 1cxpS 1kcwS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 122340.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00450, ferroxidase |
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-Myeloperoxidase ... , 2 types, 2 molecules BD
#2: Protein | Mass: 12894.465 Da / Num. of mol.: 1 / Fragment: UNP residues 165-278 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase |
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#3: Protein | Mass: 53305.266 Da / Num. of mol.: 1 / Fragment: UNP residues 279-745 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase |
-Sugars , 2 types, 5 molecules
#4: 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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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 8 molecules
#5: Chemical | ChemComp-CU / #7: Chemical | ChemComp-HEM / | |
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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: 3.61 Å3/Da / Density % sol: 65.89 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40% MPD, 0.2 M potassium fluoride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.98 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2006 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 4.69→138.68 Å / Num. all: 16100 / Num. obs: 15959 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.234 |
Reflection shell | Resolution: 4.69→4.8 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1KCW AND 1CXP Resolution: 4.69→15 Å / Cor.coef. Fo:Fc: 0.737 / Cor.coef. Fo:Fc free: 0.685 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 1.67 / ESU R Free: 1.83 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 4.69→15 Å
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LS refinement shell | Resolution: 4.69→4.801 Å / Total num. of bins used: 20
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