[English] 日本語
![](img/lk-miru.gif)
- PDB-1vlb: STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOV... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vlb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS AT 1.28 A | |||||||||
![]() | ALDEHYDE OXIDOREDUCTASE | |||||||||
![]() | OXIDOREDUCTASE / Aldehyde Oxidoreductase / Desulfovibrio Gigas / iron-sulphur cluster | |||||||||
Function / homology | ![]() aldehyde dehydrogenase (FAD-independent) / aldehyde dehydrogenase (FAD-independent) activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rebelo, J.M. / Dias, J.M. / Huber, R. / Moura, J.J.G. / Romao, M.J. | |||||||||
![]() | ![]() Title: Structure refinement of the aldehyde oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 A Authors: Rebelo, J.M. / Dias, J.M. / Huber, R. / Moura, J.J.G. / Romao, M.J. #1: ![]() Title: Structure of the Aldehyde Oxido-reductase from Desulfovibrio gigas at 2.25 A Resolution: A Member of the Xanthine Oxidase Protein Family Authors: Romao, M.J. / Archer, M. / Moura, I. / Moura, J.J.G. / LeGall, J. / Engh, R. / Schneider, M. / Hof, P. / Huber, R. #2: ![]() Title: A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes Authors: Huber, R. / Hof, P. / Duarte, R.O. / Moura, J.J.G. / Moura, I. / Liu, M.-Y. / LeGall, J. / Hille, R. / Archer, M. / Romao, M.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 414.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 335.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 494.5 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1alo S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 97140.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 6 types, 1248 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PCD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PCD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PCD / ( | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MgCl2, isopropyl alcohol, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 1998 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→24.4 Å / Num. all: 233755 / Num. obs: 226751 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.036 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.436 / % possible all: 92.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ALO ![]() 1alo Resolution: 1.28→24.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→24.4 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|