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- PDB-7c75: Crystal structure of yak lactoperoxidase with partially coordinat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c75 | |||||||||
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Title | Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity | |||||||||
![]() | 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. / Rani, C. / Ahmad, N. / 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 | ![]() | 152.4 KB | Display | ![]() |
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PDB format | ![]() | 111.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l32C ![]() 6l5gC ![]() 7c73C ![]() 7c74C ![]() 7d52C ![]() 7dmrC ![]() 6l3z 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
-Protein / Sugars , 2 types, 5 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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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 399 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-HEM / |
#5: Chemical | ChemComp-K / |
#6: Chemical | ChemComp-ZN / |
#7: Chemical | ChemComp-NA / |
#8: 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: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Sodium Fluoride, 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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 19, 2019 / Details: mirror |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→64.3 Å / Num. obs: 18790 / % possible obs: 99.3 % / Redundancy: 9.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.09 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1265 / CC1/2: 0.83 / Rpim(I) all: 0.34 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6L3Z ![]() 6l3z Resolution: 2.7→64.295 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.829 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.179 / SU B: 15.846 / SU ML: 0.311 / Average fsc free: 0.878 / Average fsc work: 0.9093 / Cross valid method: FREE R-VALUE / ESU R Free: 0.4 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: 25.515 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→64.295 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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