[English] 日本語
![](img/lk-miru.gif)
- PDB-3nbb: Crystal structure of mutant Y305F expressed in E. coli in the cop... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3nbb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha | ||||||
![]() | Peroxisomal primary amine oxidase | ||||||
![]() | OXIDOREDUCTASE / amine oxidase / quinoprotein | ||||||
Function / homology | ![]() primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Z. / Datta, S. / DuBois, J.L. / Klinman, J.P. / Mathews, F.S. | ||||||
![]() | ![]() Title: Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity. Authors: Chen, Z.W. / Datta, S. / Dubois, J.L. / Klinman, J.P. / Mathews, F.S. #1: Journal: Structure / Year: 1998 Title: Copper amine oxidase from Hansenula polymorpha: the crystal structure determined at 2.4 A resolution reveals the active conformation. Authors: Li, R. / Klinman, J.P. / Mathews, F.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 831.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 689.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 572.2 KB | Display | |
Data in XML | ![]() | 172.7 KB | Display | |
Data in CIF | ![]() | 250.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n9hC ![]() 3nbjC ![]() 1a2vS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 77696.617 Da / Num. of mol.: 6 / Mutation: Y305F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.13 % |
---|---|
Crystal grow | Temperature: 295 K / pH: 7.5 Details: 20% PEG8000, 100mM HEPES, 2% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2003 |
Radiation | Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. obs: 217301 / % possible obs: 77.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A2V Resolution: 2.05→36.13 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 217092.7 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→36.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep_tpo405.par / Topol file: protein_tpo405.top |