+Open data
-Basic information
Entry | Database: PDB / ID: 1dnu | |||||||||
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Title | STRUCTURAL ANALYSES OF HUMAN MYELOPEROXIDASE-THIOCYANATE COMPLEX | |||||||||
Components | (MYELOPEROXIDASE) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / peroxidase / inhibitor complex thiocyanate / halide peroxidation / neutrophil | |||||||||
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 / removal of superoxide radicals / defense response to fungus / response to mechanical stimulus / peroxidase activity / hydrogen peroxide catabolic process / secretory granule / 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 / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | |||||||||
Authors | Blair-Johnson, M. / Fiedler, T.J. / Fenna, R.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Human myeloperoxidase: structure of a cyanide complex and its interaction with bromide and thiocyanate substrates at 1.9 A resolution. Authors: Blair-Johnson, M. / Fiedler, T. / Fenna, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dnu.cif.gz | 258.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dnu.ent.gz | 209.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/1dnu ftp://data.pdbj.org/pub/pdb/validation_reports/dn/1dnu | HTTPS FTP |
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-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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Details | The biological assembly is a dimer composed of two pseudo-monomers made from a heavy and light chain. The symmetry partner is generated via a rotation about the noncrystallographic two-fold. |
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 11903.343 Da / Num. of mol.: 2 Fragment: MYELOPEROXIDASE LIGHT CHAIN CONTAINING RESIDUES 1 TO 104 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: MYELOPEROXIDASE HEAVY CHAIN CONTAINING RESIDUES 113 TO 578 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 #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 856 molecules
#4: Chemical | ChemComp-SCN / #5: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-ACY / #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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop with macro seeding / pH: 5.5 Details: Crystal is grown from sodium acetate, ammonium sulfate calcium chloride, and Peg MW 8000. It was subsequently equilibrated with a substitute mother liquor which contained sodium thiocyanate. ...Details: Crystal is grown from sodium acetate, ammonium sulfate calcium chloride, and Peg MW 8000. It was subsequently equilibrated with a substitute mother liquor which contained sodium thiocyanate., pH 5.5, Vapor Diffusion, Hanging Drop with Macro Seeding, temperature 22K |
-Data collection
Diffraction | Mean temperature: 84 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 108427 / Num. obs: 108318 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.139 / Num. unique all: 10720 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Resolution: 1.85→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Slow Cooling Method with Simulated Annealing and Bulk Solvent Correction
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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