[English] 日本語
![](img/lk-miru.gif)
- PDB-1d4a: CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d4a | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 A RESOLUTION | ||||||
![]() | QUINONE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD | ||||||
Function / homology | ![]() response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to nutrient / response to hormone / cell redox homeostasis / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M. | ||||||
![]() | ![]() Title: Structures of recombinant human and mouse NAD(P)H:quinone oxidoreductases: species comparison and structural changes with substrate binding and release. Authors: Faig, M. / Bianchet, M.A. / Talalay, P. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M. #1: ![]() Title: Structure and Mechanism of Cytosolic Quinone Reductase Authors: Bianchet, M.A. / Foster, C. / Faig, M. / Talalay, P. / Amzel, L.M. #2: ![]() Title: The Three-Dimensional Structure of NAD(P)H:quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M. #3: ![]() Title: Crystal Structure of Human Quinone Reductase type 2, a Metalloprotein Authors: Foster, C. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 236.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 191.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 52 KB | Display | |
Data in CIF | ![]() | 70.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30776.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30 % PEG 3350 200 MM NAACETATE 12-24 MICROM FAD 100MM NA-TRICINE PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.44 Å / Num. all: 98473 / Num. obs: 30063 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.159 / % possible all: 24.2 |
Reflection | *PLUS Num. obs: 98473 / Rmerge(I) obs: 0.052 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→43.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1344082.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.23 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.313 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.313 |