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- PDB-7dao: Crystal structure of native yak lactoperoxidase at 2.28 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dao | ||||||
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Title | Crystal structure of native yak lactoperoxidase at 2.28 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. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal structure of native yak lactoperoxidase at 2.28 A resolution Authors: Singh, P.K. / Ahmad, N. / Rani, C. / Sharma, 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 | ![]() | 151.2 KB | Display | ![]() |
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PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d52S S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#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 , 5 types, 346 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-HEM / |
#6: Chemical | ChemComp-ZN / |
#7: Chemical | ChemComp-CL / |
#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: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05M potassium 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 EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→42.621 Å / Num. obs: 30344 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.28→2.34 Å / Mean I/σ(I) obs: 2.28 / Num. unique obs: 2081 / CC1/2: 0.79 / Rrim(I) all: 0.99 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D52 Resolution: 2.28→42.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.643 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.313 / ESU R Free: 0.237 Details: Hydrogens have been used if present in the input file
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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: 50.639 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→42.62 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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