[English] 日本語
![](img/lk-miru.gif)
- PDB-5xrv: Crystal Structure of Transketolase in complex with TPP_V and fruc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xrv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Transketolase in complex with TPP_V and fructose-6-phosphate from Pichia Stipitis | ||||||
![]() | Transketolase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() purine nucleotide metabolic process / carbohydrate derivative metabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Hsu, N.S. / Wang, Y.L. | ||||||
![]() | ![]() Title: Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions. Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Ke, S.C. / Lyu, S.Y. / Hsu, L.J. / Li, Y.S. / Chen, S.C. / Wang, K.C. / Li, T.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 310.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 242.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5xpsC ![]() 5xqaC ![]() 5xqkC ![]() 5xt0C ![]() 5xt4C ![]() 5xtxC ![]() 5xu2C ![]() 5xu9C ![]() 5hyvS 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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 75054.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 936 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/F6R.gif)
![](data/chem/img/8EF.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F6R.gif)
![](data/chem/img/8EF.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-F6R / ![]() | ||||
#4: Chemical | ChemComp-8EF / | ||||
#5: Chemical | ChemComp-PEG / ![]() #6: Chemical | ChemComp-TPP / | ![]() #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.61 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→30 Å / Num. obs: 178636 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5HYV Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.286 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.786 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.4→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|