[English] 日本語
![](img/lk-miru.gif)
- PDB-3v0u: Crystal Structure of Perakine Reductase, Founder Member of a Nove... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3v0u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding | ||||||
![]() | Perakine reductase | ||||||
![]() | OXIDOREDUCTASE / Perakine Reductase / AKR superfamily | ||||||
Function / homology | ![]() perakine reductase / alkaloid metabolic process / aldo-keto reductase (NADPH) activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, L. / Chen, Y. / Rajendran, C. / Panjikar, S. / Mueller, U. / Wang, M. / Rosenthal, C. / Mindnich, R. / Penning, T.M. / Stoeckigt, J. | ||||||
![]() | ![]() Title: Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding. Authors: Sun, L. / Chen, Y. / Rajendran, C. / Mueller, U. / Panjikar, S. / Wang, M. / Mindnich, R. / Rosenthal, C. / Penning, T.M. / Stockigt, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 124.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3uyiC ![]() 3v0sC ![]() 3v0tC ![]() 1pz0S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37460.953 Da / Num. of mol.: 1 / Mutation: A213W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
---|
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→71.5 Å / Num. obs: 20584 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-
Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PZ0 Resolution: 2.203→40.634 Å / SU ML: 0.58 / σ(F): 2.01 / Phase error: 25.38 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.957 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.203→40.634 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|