[English] 日本語
![](img/lk-miru.gif)
- PDB-2vuy: Crystal structure of Glycogen Debranching exzyme TreX from Sulfol... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vuy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Glycogen Debranching exzyme TreX from Sulfolobus solfatarius | ||||||
![]() | GLYCOGEN OPERON PROTEIN GLGX | ||||||
![]() | HYDROLASE / GLYCOSIDASE / GLYCOSYL HYDROLASE | ||||||
Function / homology | ![]() glycogen debranching enzyme activity / glycogen catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / aminopeptidase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, H.-N. / Yoon, S.-M. / Cha, H.-J. / Park, K.-H. / Woo, E.-J. | ||||||
![]() | ![]() Title: Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus. Authors: Woo, E. / Lee, S. / Cha, H. / Park, J. / Yoon, S. / Song, H. / Park, K. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD", "BD" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD", "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 288.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 235.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 494.6 KB | Display | |
Data in XML | ![]() | 53.2 KB | Display | |
Data in CIF | ![]() | 70.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vncC ![]() 2vr5C ![]() 1bf2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 83181.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DISULFIDE BOND BETWEEN A254 AND A261, A505 AND A519, B254 AND B261, B505 AND B519 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P95868, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % / Description: NONE |
---|---|
Crystal grow | pH: 9.5 / Details: 16% PEG 8000, 0.2M NACL, 0.1 CHESS BUFFER(PH9.5) |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 39857 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.24 / % possible all: 95.8 |
-
Processing
Software | Name: PHASER / Classification: phasing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BF2 Resolution: 3→29.86 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |