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- PDB-2qpk: Crystal structure of the complex of bovine lactoperoxidase with s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qpk | |||||||||
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Title | Crystal structure of the complex of bovine lactoperoxidase with salicylhydroxamic acid at 2.34 A resolution | |||||||||
![]() | Lactoperoxidase | |||||||||
![]() | OXIDOREDUCTASE / Inhibitor / Complex / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Glycoprotein / Heme / Hydrogen peroxide / Iron / Metal-binding / Peroxidase / Secreted | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Singh, A.K. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P. | |||||||||
![]() | ![]() Title: Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98 angstrom resolution. Authors: Singh, P.K. / Sirohi, H.V. / Iqbal, N. / Tiwari, 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 | ![]() | 147.3 KB | Display | ![]() |
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PDB format | ![]() | 112.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tgyC ![]() 4pnxC ![]() 5b72C ![]() 5glsC ![]() 2pt3S 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 , 1 types, 1 molecules A
#1: Protein | Mass: 67853.281 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 6 types, 313 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SHA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SHA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / | ||||||||
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#5: Chemical | ChemComp-IOD / #6: Chemical | ChemComp-SCN / | #7: Chemical | ChemComp-HEM / | #8: Chemical | ChemComp-SHA / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Tris-HCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2007 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54172 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→20 Å / Num. all: 27454 / Num. obs: 26567 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.34→2.41 Å / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PT3 Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.412 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.402 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.966 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.4 Å / Total num. of bins used: 20 /
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