[English] 日本語
![](img/lk-miru.gif)
- PDB-5k42: Structure of Mycobacterium thermoresistibile trehalose-6-phosphat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5k42 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with GDP-glucose. | ||||||
![]() | Alpha,alpha-trehalose-phosphate synthase | ||||||
![]() | TRANSFERASE / OtsA trehalose-6-phosphate synthase / Trehalose | ||||||
Function / homology | ![]() alpha,alpha-trehalose-phosphate synthase (ADP-forming) / trehalose metabolism in response to stress / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / hexosyltransferase activity / cellular response to heat / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mendes, V. / Verma, N. / Blaszczyk, M. / Blundell, T.L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate. Authors: Mendes, V. / Acebron-Garcia-de-Eulate, M. / Verma, N. / Blaszczyk, M. / Dias, M.V.B. / Blundell, T.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 208.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 803.3 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jijSC ![]() 5jioC ![]() 5k41C ![]() 5k44C ![]() 5k5cC ![]() 5l3kC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 54681.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RMCT_1906 / Production host: ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-GDG / | ||
#3: Chemical | ChemComp-NHE / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.89 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 0.1M CHES pH 10 0.7M sodium potassium tartrate 10% v/v ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.92→108.41 Å / Num. obs: 64773 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 32.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Net I/σ(I): 23.1 / Num. measured all: 842990 | |||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5JIJ Resolution: 1.921→45.01 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.76
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 221.81 Å2 / Biso mean: 45.6689 Å2 / Biso min: 21.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.921→45.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|