[English] 日本語
![](img/lk-miru.gif)
- PDB-5gv7: Structure of NADH-cytochrome b5 reductase refined with the multip... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gv7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.80 A | ||||||
![]() | NADH-cytochrome b5 reductase 3 | ||||||
![]() | OXIDOREDUCTASE / electron transfer / flavoprotein | ||||||
Function / homology | ![]() cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takaba, K. / Takeda, K. / Miki, K. | ||||||
![]() | ![]() Title: Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase. Authors: Takaba, K. / Takeda, K. / Kosugi, M. / Tamada, T. / Miki, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 163.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5gv8C ![]() 1ndhS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30873.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 4000, DTT, K-phos buffer |
-Data collection
Diffraction | Mean temperature: 40 K Ambient temp details: The author used a cryo-stream of helium. |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 0.8→29.3 Å / Num. obs: 314475 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.067 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 0.8→0.81 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1NDH Resolution: 0.8→29.3 Å / Cross valid method: FREE R-VALUE Details: The model was finally refined with aspherical atomic model by using MOPRO program.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.8→29.3 Å
|