[English] 日本語
![](img/lk-miru.gif)
- PDB-1dyu: The active site base controls cofactor reactivity in Escherichia ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dyu | ||||||
---|---|---|---|---|---|---|---|
Title | The active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants. | ||||||
![]() | COPPER AMINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / TPQ / COPPER AMINE OXIDASE / EC 1.4.3.4 / WILDTYPE / CATALYTIC BASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
![]() | ![]() Title: The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase : X-Ray Crystallographicstudies with Mutational Variants Authors: Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET. SHEETS K AND K1 REPRESENT ONE BIFURCATED SHEET. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 326.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 263 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 506.5 KB | Display | |
Data in XML | ![]() | 74.4 KB | Display | |
Data in CIF | ![]() | 109.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qafC ![]() 1qakC ![]() 1qalC ![]() 1oacS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | BIOLOGICAL_UNIT: DIMERIC |
-
Components
#1: Protein | Mass: 81366.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: EACH MONOMER CONTAINS ONE COPPER ATOM, TWO CALCIUM ATOMS, AND ONE 2,4,5, -TRIHYDROXYPHENYLALANINE QUINONE COFACTOR. Source: (gene. exp.) ![]() ![]() Description: CLONED AND OVER-EXPRESSED IN E. COLI USING PLASMID PKK233-3 Cellular location: PERIPLASM / Plasmid: PLASMID DERIVED FROM PKK233-3 / Cellular location (production host): PERIPLASM / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.1 / Details: 1.2 M SODIUM CITRATE, 0.1 M HEPES PH 7.1 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20 Å / Num. obs: 105826 / % possible obs: 93.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.04→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.19 / % possible all: 91 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 91 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OAC Resolution: 2.04→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: NEITHER THE N-TERMINAL OR C-TERMINAL AMINO ACIDS WERE WELL DEFINED BY THE ELECTRON DENSITY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|