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Yorodumi- PDB-3niu: Crystal structure of the complex of dimeric goat lactoperoxidase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3niu | |||||||||
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Title | Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / LACTOPEROXIDASE / COMPLEX / DIETHYLENE GLYCOL / PHOSPHATE / MILK PROTEIN / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / peroxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / basolateral plasma membrane ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / peroxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / calcium ion binding / heme binding / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Capra hircus (goat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | |||||||||
Authors | Vikram, G. / Singh, R.P. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution Authors: Vikram, G. / Singh, R.P. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3niu.cif.gz | 260 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3niu.ent.gz | 208.8 KB | Display | PDB format |
PDBx/mmJSON format | 3niu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3niu ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3niu | HTTPS FTP |
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-Related structure data
Related structure data | 2ojvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 67609.766 Da / Num. of mol.: 2 / Fragment: residues 1-595 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS, peroxidase |
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-Sugars , 3 types, 8 molecules
#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 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 5 types, 474 molecules
#5: Chemical | ChemComp-PO4 / #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.2M Potassium dihydrogen phosphate 20%w/v PEG 3350, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 280K |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 20, 2006 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→25 Å / Num. all: 28536 / Num. obs: 28536 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OJV Resolution: 2.94→25 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.812 / SU B: 18.136 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.504 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.774 Å2
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Refinement step | Cycle: LAST / Resolution: 2.94→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.94→3.016 Å / Total num. of bins used: 20
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