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Yorodumi- PDB-5b72: Crystal structure of bovine lactoperoxidase with a broken covalen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b72 | |||||||||
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Title | Crystal structure of bovine lactoperoxidase with a broken covalent bond between Glu258 and heme moiety at 1.98 A resolution. | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / peroxidase activity / hydrogen peroxide catabolic process / 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 / peroxidase activity / hydrogen peroxide catabolic process / 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: 1.98 Å | |||||||||
Authors | Singh, P.K. / Sirohi, H.V. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2016 Title: Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98 angstrom resolution Authors: Singh, P.K. / Sirohi, H.V. / Iqbal, N. / Tiwari, P. / 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 | 5b72.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b72.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 5b72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b72 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b72 | HTTPS FTP |
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-Related structure data
Related structure data | 2qpkC 3tgyC 4pnxC 5glsC 4s0y 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: 67740.211 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Mutation: W220S, F254S, D410K, V547M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LPO / Production host: Bos taurus (cattle) / References: UniProt: P80025, peroxidase |
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-Sugars , 2 types, 4 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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#7: Sugar |
-Non-polymers , 7 types, 277 molecules
#3: Chemical | ChemComp-SO4 / | ||||||||
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#4: Chemical | ChemComp-OSM / | ||||||||
#5: Chemical | ChemComp-IOD / #6: Chemical | #8: Chemical | ChemComp-CA / | #9: Chemical | ChemComp-HEM / | #10: 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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K. PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 30, 2015 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→72.39 Å / Num. obs: 41631 / % possible obs: 96.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.15 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.98→2.01 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.1 / % possible all: 69.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S0Y 4s0y Resolution: 1.98→72.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.456 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.576 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→72.39 Å
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Refine LS restraints |
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