[English] 日本語
![](img/lk-miru.gif)
- PDB-2r4u: Crystal Structure of Wild-type E.coli GS in complex with ADP and ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2r4u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Wild-type E.coli GS in complex with ADP and Glucose(wtGSd) | ||||||
![]() | Glycogen synthase | ||||||
![]() | TRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and glucose binding | ||||||
Function / homology | ![]() starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / glycogen (starch) synthase activity / glycogen biosynthetic process / DNA damage response / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sheng, F. / Geiger, J. | ||||||
![]() | ![]() Title: The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase. Authors: Sheng, F. / Jia, X. / Yep, A. / Preiss, J. / Geiger, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 115.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qzsC ![]() 2r4tC ![]() 3copC ![]() 3d1jC ![]() 3guhC ![]() 2qyy 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 / Sugars , 2 types, 2 molecules A![](data/chem/img/GLC.gif)
![](data/chem/img/GLC.gif)
#1: Protein | Mass: 53951.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A6U8, starch synthase (glycosyl-transferring) |
---|---|
#2: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 204 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/250.gif)
![](data/chem/img/PE3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/250.gif)
![](data/chem/img/PE3.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ADP / | ||
---|---|---|---|
#4: Chemical | ChemComp-250 / ( | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.3 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 40%(w/v) PEG 4000, 0.2 M Na tartrate and 0.1 M HEPPSO (pH 7.7), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2006 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.367→97.66 Å / Num. obs: 47317 / % possible obs: 98.1 % / Observed criterion σ(I): 2.75 / Redundancy: 5.1 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.429 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.367→2.45 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.75 / Num. unique all: 4785 / Χ2: 1.018 / % possible all: 99 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 0.306 / Cor.coef. Fo:Fc: 0.785
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2QYY ![]() 2qyy Resolution: 2.367→97.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.264 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(I): 2.75 / ESU R: 0.165 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.926 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.367→97.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.367→2.429 Å / Total num. of bins used: 20
|