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- PDB-7dn6: Crystal structure of bovine lactoperoxidase with hydrogen peroxid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dn6 | |||||||||
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Title | Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution | |||||||||
![]() | Lactoperoxidase![]() | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singh, P.K. / Singh, A.K. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
![]() | ![]() Title: Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 angstrom resolution. Authors: Singh, P.K. / Sharma, P. / Bhushan, A. / 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 | ![]() | 159.9 KB | Display | ![]() |
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PDB format | ![]() | 118.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dlqC ![]() 7dn7C ![]() 3q9k 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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 3 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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#5: Sugar | ![]() |
-Non-polymers , 9 types, 682 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OSM.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OSM.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / ![]() | ||||||||||||
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#4: Chemical | ChemComp-CA / | ||||||||||||
#6: Chemical | ChemComp-IOD / ![]() #7: Chemical | ChemComp-GOL / | ![]() #8: Chemical | ChemComp-EDO / | ![]() #9: Chemical | ChemComp-ZN / | #10: Chemical | #11: Chemical | ChemComp-PEO / | ![]() #12: 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: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Ammonium Iodide, 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: MARRESEARCH / Detector: CCD / Date: Oct 21, 2010 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.696→39.41 Å / Num. obs: 70470 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rsym value: 0.079 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.696→1.74 Å / Num. unique obs: 4474 / Rsym value: 0.59 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3q9k ![]() 3q9k Resolution: 1.696→39.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.119 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: 36.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.696→39.41 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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