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Yorodumi- PDB-1d2v: CRYSTAL STRUCTURE OF BROMIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d2v | |||||||||
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Title | CRYSTAL STRUCTURE OF BROMIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5 | |||||||||
Components | (MYELOPEROXIDASE) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / HEME-PROTEIN / PEROXIDASE / PEROXIDASE-BROMIDE 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 / 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 / Resolution: 1.75 Å | |||||||||
Authors | Fiedler, T.J. / Davey, C.A. / Fenna, R.E. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: X-ray crystal structure and characterization of halide-binding sites of human myeloperoxidase at 1.8 A resolution. Authors: Fiedler, T.J. / Davey, C.A. / Fenna, R.E. #1: Journal: Arch.Biochem.Biophys. / Year: 1995 Title: Structure of the Green Heme in Myeloperoxidase Authors: Fenna, R. / Zeng, J. / Davey, C. #2: Journal: Biochemistry / Year: 1996 Title: 2.3 Angstrom Resolution X-Ray Crystal Structure of the Bisubstrate Analogue Inhibitor Salicylhydroxamic Acid Bound to Human Myeloperoxidase: A Model for a Prereaction Complex with Hydrogen Peroxide Authors: Davey, C.A. / Fenna, R.E. #3: Journal: J.Mol.Biol. / Year: 1992 Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstrom Resolution Authors: Zeng, J. / Fenna, R.E. #4: Journal: Biochem.Biophys.Res.Commun. / Year: 1994 Title: Site-Directed Mutagenesis of Human Myeloperoxidase: Further Identification of Residues Involved in Catalytic Activity and Heme Interaction Authors: Jacquet, A. / Garcia-Quintana, L. / Deleersnyder, V. / Fenna, R. / Bollen, A. / Moguilevsky, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d2v.cif.gz | 259 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d2v.ent.gz | 209.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d2v_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1d2v_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1d2v_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 1d2v_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d2v ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d2v | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.60825, 0.6773, -0.41387), Vector: |
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 11903.343 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHIL / Tissue: BLOOD / References: UniProt: P05164, peroxidase #2: Protein | Mass: 53234.191 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHIL / Tissue: BLOOD / References: UniProt: P05164, peroxidase |
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-Sugars , 2 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 852 molecules
#4: Chemical | #5: Chemical | ChemComp-BR / #6: Chemical | #7: Chemical | #9: Chemical | ChemComp-ACT / #10: Water | ChemComp-HOH / | |
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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: 2.48 Å3/Da / Density % sol: 50.45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: polyethylene glycol 8000, ammonium sulfate, sodium acetate, calcium acetate, sodium bromide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 86 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: LONG FOCUSING MIRRORS, ADSC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 117117 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.906 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.23 / % possible all: 83.6 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Num. measured all: 340410 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 83.6 % / Mean I/σ(I) obs: 6.23 |
-Processing
Software |
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Refinement | Resolution: 1.75→30 Å / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.239 / Rfactor Rfree: 0.294 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Rfactor Rfree: 0.344 / Rfactor obs: 0.293 |