[English] 日本語
![](img/lk-miru.gif)
- PDB-4h2p: Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4h2p | ||||||
---|---|---|---|---|---|---|---|
Title | Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) | ||||||
![]() | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | ||||||
![]() | OXIDOREDUCTASE / FAD-binding motif / Oxygenase / FAD / 3-hydroxypyridine-5-carboxylic acid | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Yagi, T. | ||||||
![]() | ![]() Title: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase Authors: Kobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / Kamitori, S. / Yagi, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 350.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 283.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 74 KB | Display | |
Data in CIF | ![]() | 106.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aljC ![]() 3allC ![]() 3almC ![]() 4gf7C ![]() 4h2nC ![]() 4jy2C ![]() 4jy3C ![]() 3gmbS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41798.488 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 1476 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.82 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.0M Lithium sulfate, 6% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 195890 / % possible obs: 98.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 7.8 / Num. unique all: 9302 / % possible all: 95.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GMB Resolution: 1.981→43.905 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.19 / σ(F): 1.33 / Phase error: 18.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.303 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.13 Å2 / Biso mean: 24.8726 Å2 / Biso min: 8.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.981→43.905 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|