+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h4j | ||||||
---|---|---|---|---|---|---|---|
Title | Methylobacterium extorquens methanol dehydrogenase D303E mutant | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE / DEHYDROGENASE / QUINOPROTEIN | ||||||
Function / homology | ![]() alcohol dehydrogenase (cytochrome c(L)) activity / methanol dehydrogenase (cytochrome c) / methanol oxidation / methanol metabolic process / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mohammed, F. / Gill, R. / Thompson, D. / Cooper, J.B. / Wood, S.P. / Afolabi, P.R. / Anthony, C. | ||||||
![]() | ![]() Title: Site-Directed Mutagenesis and X-Ray Crystallography of the Pqq-Containing Quinoprotein Methanol Dehydrogenase and its Electron Acceptor, Cytochrome C(L)(,) Authors: Afolabi, P.R. / Mohammed, F. / Amaratunga, K. / Majekodunmi, O. / Dales, S.L. / Gill, R. / Thompson, D. / Cooper, J.B. / Wood, S.P. / Goodwin, P.M. / Anthony, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 500.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 410.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 95.3 KB | Display | |
Data in CIF | ![]() | 124.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 65880.859 Da / Num. of mol.: 4 / Mutation: D303E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P16027, methanol dehydrogenase (cytochrome c) #2: Protein | Mass: 8480.620 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRROLO-QUINOLINE QUINONE PROSTHETIC GROUP WITH ACTIVE SITE CALCIUM IONS Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14775, methanol dehydrogenase (cytochrome c) #3: Chemical | ChemComp-PQQ / #4: Chemical | ChemComp-CA / Compound details | CHAIN A, C, E, G ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 9.5 / Details: pH 9.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 9.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 48502 / % possible obs: 91.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.6 / % possible all: 81.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 134792 |
Reflection shell | *PLUS % possible obs: 81.4 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: WILD-TYPE STRUCTURE Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |