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Yorodumi- PDB-9it8: Crystal structure of the ternary complex of lactoperoxidase with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9it8 | ||||||
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Title | Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution | ||||||
Components | Lactoperoxidase | ||||||
Keywords | OXIDOREDUCTASE / Bovine lactoperoxidase / Peroxide family | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å | ||||||
Authors | Maurya, A. / Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution Authors: Maurya, A. / Ahmad, N. / Sharma, 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 | 9it8.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9it8.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 9it8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9it8_validation.pdf.gz | 13.5 MB | Display | wwPDB validaton report |
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Full document | 9it8_full_validation.pdf.gz | 13.6 MB | Display | |
Data in XML | 9it8_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 9it8_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/9it8 ftp://data.pdbj.org/pub/pdb/validation_reports/it/9it8 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, 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 , 10 types, 377 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NO3 / #7: Chemical | ChemComp-SCN / #8: Chemical | ChemComp-IOD / #9: Chemical | ChemComp-HEM / | #10: Chemical | ChemComp-EDO / | #11: Chemical | ChemComp-CA / | #12: Chemical | ChemComp-OSM / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M AMMONIUM IODIDE, 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→74.05 Å / Num. obs: 45886 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.094 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3093 / CC1/2: 0.658 / Rpim(I) all: 0.725 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.954→74.049 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.169 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: 53.701 Å2
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Refinement step | Cycle: LAST / Resolution: 1.954→74.049 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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