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- PDB-7c74: Crystal structure of yak lactoperoxidase using data obtained from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c74 | |||||||||
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Title | Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in CaCl2 at 2.73 A resolution | |||||||||
![]() | Lactoperoxidase | |||||||||
![]() | OXIDOREDUCTASE / Lactoperoxidase | |||||||||
Function / homology | ![]() thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / basolateral plasma membrane / response to oxidative stress / defense response to bacterium / heme binding / extracellular space / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singh, P.K. / Viswanathan, V. / Pandey, S.N. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, P. / Singh, T.P. | |||||||||
![]() | ![]() Title: Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution. Authors: Singh, P.K. / Pandey, S. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / 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 | ![]() | 147.5 KB | Display | ![]() |
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PDB format | ![]() | 108.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.1 KB | Display | ![]() |
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Full document | ![]() | 835.5 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l32C ![]() 6l5gC ![]() 7c73C ![]() 7c75C ![]() 7d52C ![]() 7dmrC ![]() 6lo7 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M CaCl2, 20% PEG 3350 / PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2019 / Details: mirror |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→53.01 Å / Num. obs: 16875 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.96 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.079 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.73→2.8 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3 / Num. unique obs: 1174 / CC1/2: 0.94 / Rpim(I) all: 0.197 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LO7 ![]() 6lo7 Resolution: 2.73→53.01 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.826 / SU B: 18.094 / SU ML: 0.357 / Cross valid method: FREE R-VALUE / ESU R Free: 0.459 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: 31.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→53.01 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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