+
Open data
-
Basic information
Entry | Database: PDB / ID: 1an9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | D-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE | |||||||||
![]() | D-AMINO ACID OXIDASE | |||||||||
![]() | OXIDOREDUCTASE / FAD / OXIDASE / D-AMINO ACID / FLAVOPROTEIN | |||||||||
Function / homology | ![]() Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone ...Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / peroxisome / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Miura, R. / Setoyama, C. / Nishina, Y. / Shiga, K. / Mizutani, H. / Miyahara, I. / Hirotsu, K. | |||||||||
![]() | ![]() Title: Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex. Authors: Miura, R. / Setoyama, C. / Nishina, Y. / Shiga, K. / Mizutani, H. / Miyahara, I. / Hirotsu, K. #1: ![]() Title: Three-Dimensional Structure of Porcine Kidney D-Amino Acid Oxidase at 3.0 A Resolution Authors: Mizutani, H. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Miura, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 150.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 118.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 546.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 565.7 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aa8 S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38612.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.3 Details: PROTEIN WAS CRYSTALLIZED FROM 120MM SODIUM ACETATE, 60MM SODIUM CITRATE, 30% PEG4000, pH 6.3 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: Setoyama, C., (1996) J. Biochem., 119, 1114. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 22424 / % possible obs: 87.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.5→2.61 Å / % possible all: 73.32 |
Reflection | *PLUS Num. measured all: 66408 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AA8 ![]() 1aa8 Resolution: 2.5→10 Å / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|