[English] 日本語
![](img/lk-miru.gif)
- PDB-1wm6: Crystal structure of TT0310 protein from Thermus thermophilus HB8 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1wm6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TT0310 protein from Thermus thermophilus HB8 | ||||||
![]() | phenylacetic acid degradation protein PaaI | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thioesterase / Hot dog fold / Phenylacetic acid degradation / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugahara, M. / Kunishima, N. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI Authors: Kunishima, N. / Asada, Y. / Sugahara, M. / Ishijima, J. / Nodake, Y. / Sugahara, M. / Miyano, M. / Kuramitsu, S. / Yokoyama, S. / Sugahara, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 477.7 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j1yC ![]() 1wluC ![]() 1wlvC ![]() 1wn3C C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a tetramer for instance composed of A, B, C and D subunits in the asymmetric unit. |
-
Components
#1: Protein | Mass: 14280.224 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.6 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 Details: Sodium acetate trihydrate, sodium cacodylate, pH 6.5, Microbatch, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 81420 / Num. obs: 80972 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 43.13 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8017 / % possible all: 99.6 |
Reflection | *PLUS % possible obs: 100 % |
Reflection shell | *PLUS % possible obs: 99.6 % / Redundancy: 5.6 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.7 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.014
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.7 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.267 / Rfactor obs: 0.267 |