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Yorodumi- PDB-7dn6: Crystal structure of bovine lactoperoxidase with hydrogen peroxid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dn6 | |||||||||
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Title | Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / Lactoperoxidase | |||||||||
Function / homology | Function and homology information Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding / heme binding / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å | |||||||||
Authors | Singh, P.K. / Singh, A.K. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2021 Title: Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 angstrom resolution. Authors: Singh, P.K. / Sharma, P. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dn6.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dn6.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/7dn6 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/7dn6 | HTTPS FTP |
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-Related structure data
Related structure data | 7dlqC 7dn7C 3q9k S: Starting model for refinement C: citing same article (ref.) |
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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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, peroxidase |
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-Sugars , 2 types, 3 molecules
#2: 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 |
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#5: Sugar |
-Non-polymers , 9 types, 682 molecules
#3: Chemical | ChemComp-HEM / | ||||||||||||
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#4: Chemical | ChemComp-CA / | ||||||||||||
#6: Chemical | ChemComp-IOD / #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-EDO / | #9: Chemical | ChemComp-ZN / | #10: Chemical | #11: Chemical | ChemComp-PEO / | #12: Water | ChemComp-HOH / | |
-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: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Ammonium Iodide, PEG 3350 / PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 21, 2010 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.696→39.41 Å / Num. obs: 70470 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rsym value: 0.079 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.696→1.74 Å / Num. unique obs: 4474 / Rsym value: 0.59 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3q9k 3q9k Resolution: 1.696→39.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.119 Details: Hydrogens have been added in their riding positions
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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: 36.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.696→39.41 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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