[English] 日本語
![](img/lk-miru.gif)
- PDB-5brq: Crystal structure of Bacillus licheniformis trehalose-6-phosphate... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5brq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Bacillus licheniformis trehalose-6-phosphate hydrolase (TreA) | ||||||
![]() | Glycoside Hydrolase Family 13 | ||||||
![]() | HYDROLASE / trehalose-6-phosphate hydrolase / TIM barrel / GH13 family | ||||||
Function / homology | ![]() alpha,alpha-phosphotrehalase activity / trehalose catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, C.-D. / Lin, M.-G. | ||||||
![]() | ![]() Title: Bacillus licheniformis trehalose-6-phosphate hydrolase structures suggest keys to substrate specificity Authors: Lin, M.-G. / Chi, M.-C. / Naveen, V. / Li, Y.-C. / Lin, L.-L. / Hsiao, C.-D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 488.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 396.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 469.4 KB | Display | |
Data in XML | ![]() | 87.4 KB | Display | |
Data in CIF | ![]() | 129 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5brpC ![]() 1uokS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 66642.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 14580 = DSM 13 / Gene: treA, BL03069 / Plasmid: pQE30 / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% (w/v) PEG 3350, 0.2 M magnesium acetate hexahydrate, 2% Tacsimate (pH 5.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.903 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 149079 / % possible obs: 96.8 % / Redundancy: 3.8 % / Net I/σ(I): 29 |
-
Processing
Software | Name: PHENIX / Version: 1.8.1_1168 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1UOK Resolution: 2.003→24.304 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.73 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.003→24.304 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|