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- PDB-1d5l: CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d5l | |||||||||
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Title | CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5 | |||||||||
![]() | (MYELOPEROXIDASE) x 2 | |||||||||
![]() | OXIDOREDUCTASE / HEME-PROTEIN / PEROXIDASE / PEROXIDASE-CYANIDE COMPLEX | |||||||||
Function / homology | ![]() 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 / defense response / peroxidase activity / 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 | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Fiedler, T.J. / Davey, C.A. / Fenna, R.E. | |||||||||
![]() | ![]() 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. #1: ![]() Title: Structure of the Green Heme in Myeloperoxidase Authors: Fenna, R. / Zeng, J. / Davey, C. #2: ![]() 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: ![]() Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstrom Resolution Authors: Zeng, J. / Fenna, R.E. #4: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.2 KB | Display | ![]() |
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PDB format | ![]() | 211 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 51 KB | Display | |
Data in CIF | ![]() | 74.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: (-0.60923, 0.68033, -0.40742), Vector: |
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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) ![]() #2: Protein | Mass: 53234.191 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 886 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CYN / #7: Chemical | #9: Chemical | #10: Chemical | ChemComp-ACT / #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 chloride, sodium cyanide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Details: Davey, C.A., (1996) Biochemistry, 35, 10967. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 87 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 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: 1.9→50 Å / Num. obs: 97701 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.641 % / Biso Wilson estimate: 12.93 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.38 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.61 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6.38 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 258017 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 97.5 % |
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Processing
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Refinement | Resolution: 1.9→30 Å / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.225 / Rfactor obs: 0.225 |