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Yorodumi- PDB-2e9e: Crystal structure of the complex of goat lactoperoxidase with Nit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e9e | |||||||||
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Title | Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | METAL BINDING PROTEIN / OXIDOREDUCTASE / lactoperoxidase / complex / nitrate / milk 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||
Authors | Singh, A.K. / Prem kumar, R. / Singh, N. / Sharma, S. / Singh, S.B. / Bhushan, A. / Kaur, P. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution Authors: Singh, A.K. / Prem kumar, R. / Singh, N. / Sharma, S. / Singh, S.B. / Bhushan, A. / Kaur, P. / 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 | 2e9e.cif.gz | 262.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e9e.ent.gz | 211.1 KB | Display | PDB format |
PDBx/mmJSON format | 2e9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e9e ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e9e | HTTPS FTP |
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-Related structure data
Related structure data | 2gj1 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: 67529.781 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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 8 types, 393 molecules
#5: Chemical | ChemComp-NO3 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CYN / | #9: Chemical | ChemComp-SCN / | #10: Chemical | #11: Chemical | ChemComp-OSM / | #12: 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: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: TRIS HYDROCHLORIDE, pH 8.2, 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: 1.414 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2006 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.414 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→20 Å / Num. all: 19863 / Num. obs: 19863 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.154 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 3.25→3.31 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.278 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GJ1 2gj1 Resolution: 3.25→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.87 / SU B: 18.816 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.545 / 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: 18.726 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.332 Å / Total num. of bins used: 20
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