[English] 日本語
![](img/lk-miru.gif)
- PDB-5equ: Crystal structure of the epimerase SnoN in complex with Fe3+, alp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5equ | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and nogalamycin RO | |||||||||
![]() | SnoN,SnoN | |||||||||
![]() | ISOMERASE / none-heme iron / substrate complex / nogalamycin biosynthesis | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Selvaraj, B. / Lindqvist, Y. / Siitonen, V. / Metsa-Ketela, M. / Schneider, G. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() Title: Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway. Authors: Siitonen, V. / Selvaraj, B. / Niiranen, L. / Lindqvist, Y. / Schneider, G. / Metsa-Ketela, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 417.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 342.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5ep9SC ![]() 5epaC ![]() 5erlC 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: 33079.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-5R6 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG3350, ammonium acetate, BIS-Tris, FeCl3, alpha-ketoglutarate, nogalamycin RO PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→96 Å / Num. all: 69960 / Num. obs: 69960 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.3 / Num. measured all: 282204 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.4 / % possible all: 97 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5EP9 Resolution: 2.2→95.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 17.954 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.924 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→95.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|