[English] 日本語
![](img/lk-miru.gif)
- PDB-6grr: Crystal structure of Escherichia coli amine oxidase mutant I342F/E573Q -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6grr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Escherichia coli amine oxidase mutant I342F/E573Q | ||||||
![]() | (Amine oxidase) x 2 | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() : / : / : / Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process ...: / : / : / Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Oxygen Activation Switch in the Copper Amine Oxidase of Escherichia coli. Authors: Gaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 327.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 256.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 60.4 KB | Display | |
Data in CIF | ![]() | 91.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ezzC ![]() 1dyuS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 80405.719 Da / Num. of mol.: 1 / Mutation: I342F, E573Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A2K0PX72, UniProt: P46883*PLUS, Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor |
---|---|
#2: Protein | Mass: 80673.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A2K0PX72, UniProt: P46883*PLUS, Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor |
-Non-polymers , 4 types, 1220 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.92 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES, 1.2 M sodium citrate / PH range: 6.9 - 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→105.05 Å / Num. obs: 196242 / % possible obs: 99.2 % / Redundancy: 5.1 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9515 / CC1/2: 0.873 / Rpim(I) all: 0.379 / Rrim(I) all: 0.875 / % possible all: 97.06 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DYU Resolution: 1.7→105.05 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.588 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.255 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→105.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|