[English] 日本語
Yorodumi- PDB-1c0p: D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c0p | ||||||
---|---|---|---|---|---|---|---|
Title | D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES | ||||||
Components | D-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA-ALPHA MOTIF / FLAVIN CONTAINING PROTEIN / OXIDASE | ||||||
Function / homology | Function and homology information D-glutamate oxidase activity / D-aspartate oxidase activity / D-amino acid metabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / nitrogen utilization / D-amino acid catabolic process / aspartate catabolic process / peroxisomal matrix / FAD binding / peroxisome Similarity search - Function | ||||||
Biological species | Rhodosporidium toruloides (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | ||||||
Authors | Umhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, S.M. / Ghisla, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Authors: Umhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, M.S. / Ghisla, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c0p.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c0p.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c0p_validation.pdf.gz | 724.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1c0p_full_validation.pdf.gz | 733.7 KB | Display | |
Data in XML | 1c0p_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 1c0p_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c0p ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c0p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39614.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodosporidium toruloides (fungus) / Plasmid: PT7.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80324, D-amino-acid oxidase |
---|
-Non-polymers , 5 types, 616 molecules
#2: Chemical | ChemComp-FAD / |
---|---|
#3: Chemical | ChemComp-DAL / |
#4: Chemical | ChemComp-PER / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.85 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 MM HEPES 200 MM AMMONIUM SULFATE 16% POLYETHYLENE GLYCOL (PEG) 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9114 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9114 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→100 Å / Num. all: 1000770 / Num. obs: 155642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.2→1.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.524 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.2 Å / Num. measured all: 1000779 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.2→100 Å / σ(F): 4 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→100 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 100 Å / σ(F): 4 / Rfactor obs: 0.118 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.116 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.57 |