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- PDB-8y9x: Crystal structure of the complex of lactoperoxidase with four ino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8y9x | |||||||||
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Title | Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl | |||||||||
![]() | Lactoperoxidase | |||||||||
![]() | OXIDOREDUCTASE | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Viswanathan, V. / Singh, A.K. / Pandey, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural evidence for the order of preference of inorganic substrates in mammalian heme peroxidases: crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl Authors: Viswanathan, V. / Singh, A.K. / Pandey, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.7 MB | Display | ![]() |
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Full document | ![]() | 9.8 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k5m S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 7 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 434 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||||||
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#3: Chemical | ChemComp-CA / | ||||||||||
#4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-BR / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-SCN / #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.2 M Ammonium iodide, 20%(w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298 K |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→43.521 Å / Num. obs: 39294 / % possible obs: 96.7 % / Redundancy: 6.2 % / Rsym value: 0.082 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.99→2.05 Å / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3044 / Rsym value: 0.31 / % possible all: 77 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8K5M ![]() 8k5m Resolution: 2→43.521 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.143 / SU B: 3.736 / SU ML: 0.104 / Average fsc free: 0.9733 / Average fsc work: 0.9842 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.152 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: 29.645 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.521 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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