+Open data
-Basic information
Entry | Database: PDB / ID: 8t8a | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of arginine oxidase from Pseudomonas sp. TRU 7192 | ||||||
Components | Amine oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / oxidase / arginine oxidase | ||||||
Function / homology | polyamine oxidase activity / polyamine catabolic process / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / peroxisome / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidoreductase Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Takahashi, K. / Yamaguchi, H. / Tatsumi, M. / Sugiki, M. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: Structural basis of arginine oxidase from Pseudomonas sp. TRU 7192 Authors: Yamaguchi, H. / Numoto, N. / Suzuki, H. / Nishikawa, K. / Kamegawa, A. / Takahashi, K. / Matsui, D. / Asano, Y. / Tatsumi, M. / Sugiki, M. / Fujiyoshi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8t8a.cif.gz | 454.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8t8a.ent.gz | 364.8 KB | Display | PDB format |
PDBx/mmJSON format | 8t8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t8a_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8t8a_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8t8a_validation.xml.gz | 85.7 KB | Display | |
Data in CIF | 8t8a_validation.cif.gz | 114.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/8t8a ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t8a | HTTPS FTP |
-Related structure data
Related structure data | 8jt7C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 67423.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: TPU 7192 / Gene: AYO28_23740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A177SH44 #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.45 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Potassium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→49.23 Å / Num. obs: 39436 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.346 / Rpim(I) all: 0.144 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.4→3.47 Å / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4532 / Rpim(I) all: 0.401 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.845 / SU B: 50.64 / SU ML: 0.749 / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 82.559 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→49.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|