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- PDB-4pnx: Crystal structure of the complex of lactoperoxidase with bromo me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pnx | ||||||
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Title | Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 angstrom resolution | ||||||
![]() | Lactoperoxidase | ||||||
![]() | OXIDOREDUCTASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sirohi, H.V. / Tyagi, T.K. / Singh, A.K. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / 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 | ![]() | 138.5 KB | Display | ![]() |
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PDB format | ![]() | 106.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 870.4 KB | Display | ![]() |
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Full document | ![]() | 899.7 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qpkC ![]() 3tgyC ![]() 5b72C ![]() 5glsC ![]() 3ogw 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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1 |
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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: 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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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 127 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/BMM.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/BMM.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-HEM / | ||
#5: Chemical | ChemComp-BMM / | ||
#6: Chemical | ChemComp-IOD / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 2013 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→71.16 Å / Num. all: 23328 / Num. obs: 23328 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.129 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.41→2.47 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.379 / % possible all: 92.3 |
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Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3OGW ![]() 3ogw Resolution: 2.41→71.15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.748 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.861 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→71.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.413→2.476 Å / Total num. of bins used: 20
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