[English] 日本語
![](img/lk-miru.gif)
- PDB-1dii: CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dii | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION | |||||||||
![]() | (P-CRESOL METHYLHYDROXYLASE) x 2 | |||||||||
![]() | OXIDOREDUCTASE / FLAVOCYTOCHROME / ELECTRON-TRANSFER / FAD / HEME | |||||||||
Function / homology | ![]() 4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Cunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S. | |||||||||
![]() | ![]() Title: Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. Authors: Cunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S. #1: ![]() Title: Three-dimensional Structure of p-Cresol Methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 A Resolution Authors: Mathews, F.S. / Chen, Z.W. / Bellamy, H. / McIntire, W.S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 248.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 207.5 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 | ![]() | 48.3 KB | Display | |
Data in CIF | ![]() | 67 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | ASYMMETRIC UNIT CONTAINS A FLAVOPROTEIN DIMER RELATED BY A MOLECULAR 2-FOLD AXIS. TWO CYTOCHROME SUBUNITS ARE BOUND ON THE PERIPHERY OF THE FLAVOPROTEIN DIMER. |
-
Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 58005.965 Da / Num. of mol.: 2 / Fragment: FLAVOPROTEIN SUBUNIT / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 8611.642 Da / Num. of mol.: 2 / Fragment: CYTOCHROME SUBUNIT / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 4 types, 391 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7 Details: PEG 8000, NA/K PHOSPHATE, NACL, pH 7.0, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: or interface diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: May 31, 1990 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 47875 / Num. obs: 42484 / % possible obs: 89.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.224 / % possible all: 87 |
Reflection shell | *PLUS % possible obs: 87 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.86 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.287 |