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Yorodumi- PDB-4oek: Crystal Structure of the Complex of goat Lactoperoxidase with Phe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oek | |||||||||
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Title | Crystal Structure of the Complex of goat Lactoperoxidase with Phenylethylamine at 2.47 A Resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / Peroxidase | |||||||||
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 / hydrogen peroxide catabolic process / peroxidase activity / 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 / hydrogen peroxide catabolic process / peroxidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | |||||||||
Authors | Kumar, M. / Singh, R.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex of goat Lactoperoxidase with Phenylethylamine at 2.47 A Authors: Kumar, M. / Singh, R.P. / Sinha, M. / Bhushan, A. / 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 | 4oek.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oek.ent.gz | 204.3 KB | Display | PDB format |
PDBx/mmJSON format | 4oek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oek_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4oek_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4oek_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 4oek_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oek ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oek | HTTPS FTP |
-Related structure data
Related structure data | 3sxvS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 67609.766 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS, peroxidase |
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-Sugars , 2 types, 4 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 |
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#3: Sugar |
-Non-polymers , 7 types, 272 molecules
#4: Chemical | ChemComp-HEM / | ||||||||
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#5: Chemical | ChemComp-CA / | ||||||||
#6: Chemical | ChemComp-IOD / #7: Chemical | ChemComp-SCN / | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PEA / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 298 K / pH: 6.8 Details: Sodium nitrate, PEG , pH 6.8 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 29, 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: 2.47→74.21 Å / Num. obs: 18577 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Rsym value: 0.081 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.47→2.54 Å / Mean I/σ(I) obs: 4.9 / Rsym value: 0.299 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SXV Resolution: 2.47→73.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.721 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / 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: 44.161 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→73.69 Å
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