[English] 日本語
![](img/lk-miru.gif)
- PDB-5zdp: Crystal structure of cyanide-insensitive alternative oxidase from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zdp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ferulenol | ||||||
![]() | Alternative oxidase, mitochondrial | ||||||
![]() | MEMBRANE PROTEIN / MEMBRANE BOUND DIIRON PROTEIN | ||||||
Function / homology | ![]() alternative oxidase activity / alternative respiration / Oxidoreductases / : / ferric iron binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. ...Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K. | ||||||
![]() | ![]() Title: Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. Authors: Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 230.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 185 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 41.5 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zdqC ![]() 5zdrC ![]() 3vv9S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 2 / Auth seq-ID: 33 - 601 / Label seq-ID: 33
NCS ensembles :
NCS oper:
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37643.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 90 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/9AU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/9AU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-OH / #4: Chemical | ChemComp-OXY / #5: Chemical | ChemComp-9AU / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 30% PEG400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 1, 2014 | |||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 52186 / % possible obs: 98.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.8 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2576 / % possible all: 98.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3VV9 Resolution: 2.71→39.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.263 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.065 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.215 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.71→39.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|