[English] 日本語
![](img/lk-miru.gif)
- PDB-1cwy: CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1cwy | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCOSYLTRANSFERASE CATALYSING THE PRODUCTION OF LARGE CYCLIC GLUCANS | ||||||
![]() | AMYLOMALTASE | ||||||
![]() | TRANSFERASE / (BETA / ALPHA)8 BARREL | ||||||
Function / homology | ![]() 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Przylas, I. / Tomoo, K. / Terada, Y. / Takaha, T. / Fuji, K. / Saenger, W. / Straeter, N. | ||||||
![]() | ![]() Title: Crystal structure of amylomaltase from thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. Authors: Przylas, I. / Tomoo, K. / Terada, Y. / Takaha, T. / Fujii, K. / Saenger, W. / Strater, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 128.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 362.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 365.7 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 57293.039 Da / Num. of mol.: 1 / Fragment: MALQ Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: STARTING PLASMID PGEX-NDE, FINAL PLASMID WITH CLONED GENE PFQG8 Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 65.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ETHYLENE GLYCOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 56277 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 7.4 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.8 / Rsym value: 33.7 / % possible all: 93.1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Num. measured all: 347606 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 93.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.337 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: CNS_TOPPAR/PROTEIN_REP.PARAM CNS_ TOPPAR/WATER_REP.PARAM
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.04 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→500 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / % reflection Rfree: 5.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.303 |