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Yorodumi- PDB-3eri: First structural evidence of substrate specificity in mammalian p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eri | |||||||||
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Title | First structural evidence of substrate specificity in mammalian peroxidases: Crystal structures of substrate complexes with lactoperoxidases from two different species | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / lactopeoxidase / complex / heme / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Glycoprotein / Hydrogen peroxide / Iron / Metal-binding / Peroxidase / Secreted | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Singh, A.K. / Singh, N. / Sheikh, I.A. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Evidence of Substrate Specificity in Mammalian Peroxidases: STRUCTURE OF THE THIOCYANATE COMPLEX WITH LACTOPEROXIDASE AND ITS INTERACTIONS AT 2.4 A RESOLUTION Authors: Sheikh, I.A. / Singh, A.K. / Singh, N. / Sinha, M. / Singh, S.B. / Bhushan, A. / Kaur, P. / Srinivasan, A. / 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 | 3eri.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eri.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3eri ftp://data.pdbj.org/pub/pdb/validation_reports/er/3eri | HTTPS FTP |
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-Related structure data
Related structure data | 3erhC 3faqC 2r5lS 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: 67853.281 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, peroxidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 350 molecules
#5: Chemical | ChemComp-HEM / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-IOD / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10mM phosphate buffer, 2mM CaCl2, 0.2M ammonium Iodide, 20% PEG3350, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54132 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 5, 2008 / Details: Mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54132 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.48 Å / Num. all: 23422 / Num. obs: 21599 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45.3 Å2 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R5L Resolution: 2.5→19.48 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 47803.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.5646 Å2 / ksol: 0.290064 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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