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Yorodumi- PDB-6l32: Crystal structure of potassium induced heme modification in yak l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l32 | |||||||||
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Title | Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.30 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / Lactoperoxidase | |||||||||
Function / homology | Function and homology information thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / basolateral plasma membrane / response to oxidative stress / defense response to bacterium / heme binding / extracellular space / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos mutus (wild yak) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Singh, P.K. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2021 Title: Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution. Authors: Singh, P.K. / Pandey, S. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / 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 | 6l32.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l32.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 6l32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/6l32 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/6l32 | HTTPS FTP |
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-Related structure data
Related structure data | 6l5gC 7c73C 7c74C 7c75C 7d52C 7dmrC 3bxiS S: Starting model for refinement C: citing same article (ref.) |
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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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos mutus (wild yak) / References: UniProt: L8ICE9 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | #3: Sugar | |
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-Non-polymers , 5 types, 334 molecules
#4: Chemical | ChemComp-CA / | ||||
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#5: Chemical | ChemComp-HEM / | ||||
#6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M potassium fluoride, 20% PEG 3350 / PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 9, 2019 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.114 Å / Num. obs: 30425 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.98 / Rsym value: 0.2 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3148 / CC1/2: 0.88 / Rsym value: 0.85 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BXI Resolution: 2.3→58.11 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.515 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.341 / ESU R Free: 0.238 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.013 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→58.11 Å
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Refine LS restraints |
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LS refinement shell |
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