[English] 日本語
![](img/lk-miru.gif)
- PDB-4m2j: Crystal structure of PLP-dependent cyclase OrfR in complex with Au -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4m2j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PLP-dependent cyclase OrfR in complex with Au | ||||||
![]() | Aminotransferase | ||||||
![]() | TRANSFERASE / cyclase / PLP binding | ||||||
Function / homology | ![]() Lyases; Carbon-nitrogen lyases; Amidine-lyases / transaminase activity / biosynthetic process / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, C.Y. / Liu, Y.C. / Lyu, S.Y. / Wu, C.C. / Li, T.L. | ||||||
![]() | ![]() Title: Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms. Authors: Chang, C.Y. / Lyu, S.Y. / Liu, Y.C. / Hsu, N.S. / Wu, C.C. / Tang, C.F. / Lin, K.H. / Ho, J.Y. / Wu, C.J. / Tsai, M.D. / Li, T.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.6 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m23C ![]() 4m25C ![]() 4m26C ![]() 4m27C ![]() 4m2cC ![]() 4m2eC ![]() 4m2fC ![]() 4m2gC ![]() 4m2iC ![]() 4m2kC ![]() 4m2mC ![]() 4ne0C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43720.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-AU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 100mM Bis-Tris propane, 1M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MX300HE / Detector: CCD / Date: Jun 21, 2013 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0402 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. all: 11885 / Num. obs: 11289 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.95→3.06 Å / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.564 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|