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- PDB-7c73: 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: 7c73 | |||||||||
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Title | Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 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. / Pandey, S.N. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / Kaur, P. / Sharma, S. / 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 | ![]() | 148 KB | Display | ![]() |
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PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l32C ![]() 6l5gC ![]() 7c74C ![]() 7c75C ![]() 7d52C ![]() 7dmrC ![]() 6lnv 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: 67853.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M CaCl2, 20% PEG 3350, tris-HCl, pH 8 / PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2019 / Details: MIRROR |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17274 / % possible obs: 98 % / Redundancy: 3.1 % / CC1/2: 0.96 / Rmerge(I) obs: 0.198 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.96 / Num. unique obs: 1170 / CC1/2: 0.536 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LNV ![]() 6lnv Resolution: 2.7→47.577 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.819 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.194 / SU B: 23.703 / SU ML: 0.455 / Average fsc free: 0.8066 / Average fsc work: 0.8408 / Cross valid method: FREE R-VALUE / ESU R Free: 0.479 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: 35.678 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→47.577 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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