[English] 日本語
![](img/lk-miru.gif)
- PDB-1bt2: CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE RED... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1bt2 | ||||||
---|---|---|---|---|---|---|---|
Title | CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE | ||||||
![]() | PROTEIN (CATECHOL OXIDASE) | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Klabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B. | ||||||
![]() | ![]() Title: Crystal structure of a plant catechol oxidase containing a dicopper center. Authors: Klabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99998, -0.005017, 0.003781), Vector ![]() |
-
Components
#1: Protein | Mass: 38814.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COVALENT THIOETHER BOND BETWEEN H109 AND C92 / Source: (natural) ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.34 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 ...Details: CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→20 Å / Num. obs: 18524 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.055 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Rsym value: 0.106 / % possible all: 90.4 |
Reflection | *PLUS Num. measured all: 50613 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 90.4 % / Rmerge(I) obs: 0.106 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Details: RESIDUES INVOLVED IN PACKING INTERACTIONS WERE EXCLUDED FROM THE NCS RESTRAINTS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 0.09 Å / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 |