[English] 日本語
Yorodumi- PDB-3tgy: Crystal structure of the complex of Bovine Lactoperoxidase with A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tgy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex of Bovine Lactoperoxidase with Ascorbic acid at 2.35 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE / Lactoperoxidase / ascorbic acid / glycoprotein / heme moiety / ferric iron | |||||||||
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: 2.35 Å | |||||||||
Authors | Yamini, S. / Singh, R.P. / Singh, A.K. / Pandey, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2017 Title: Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98 angstrom resolution. Authors: Singh, P.K. / Sirohi, H.V. / Iqbal, N. / Tiwari, P. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tgy.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tgy.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tgy_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tgy_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3tgy_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 3tgy_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tgy ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tgy | HTTPS FTP |
-Related structure data
Related structure data | 2qpkC 4pnxC 5b72C 5glsC 3gc1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 67853.281 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 118-712 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, peroxidase |
---|
-Sugars , 3 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | #12: Sugar | ChemComp-ASC / | |
---|
-Non-polymers , 9 types, 393 molecules
#3: Chemical | ChemComp-CA / | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-HEM / | ||||||||||||
#6: Chemical | ChemComp-IOD / #7: Chemical | ChemComp-MPD / ( | #8: Chemical | ChemComp-EDO / | #9: Chemical | ChemComp-PEG / | #10: Chemical | ChemComp-GOL / | #11: Chemical | ChemComp-SCN / | #13: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: AMMONIUM IODIDE, PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 16, 2011 / 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: 2.35→50 Å / Num. all: 20803 / Num. obs: 20803 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.35→2.39 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.23 / % possible all: 59.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GC1 Resolution: 2.35→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1691003.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.0719 Å2 / ksol: 0.317104 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|