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Yorodumi- PDB-5gls: Structure of bovine Lactoperoxidase with a partially modified cov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gls | ||||||||||||
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Title | Structure of bovine Lactoperoxidase with a partially modified covalent bond with heme moiety | ||||||||||||
Components | Lactoperoxidase | ||||||||||||
Keywords | OXIDOREDUCTASE | ||||||||||||
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: 1.93 Å | ||||||||||||
Authors | Tiwari, P. / 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 | 5gls.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gls.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/5gls ftp://data.pdbj.org/pub/pdb/validation_reports/gl/5gls | HTTPS FTP |
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-Related structure data
Related structure data | 2qpkC 3tgyC 4pnxC 5b72C 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: 67839.344 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, 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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#3: Sugar |
-Non-polymers , 7 types, 370 molecules
#4: Chemical | ChemComp-CA / | ||||||
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#5: Chemical | ChemComp-HEM / | ||||||
#6: Chemical | ChemComp-SCN / | ||||||
#7: Chemical | ChemComp-IOD / #8: Chemical | #9: Chemical | ChemComp-GOL / | #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: 2.32 Å3/Da / Density % sol: 47 % / Description: rectangular |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Ammonium Iodide, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2014 / 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: 1.93→50 Å / Num. obs: 47548 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.08 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S0Y 4s0y Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.743 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.953 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→50 Å
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Refine LS restraints |
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