[English] 日本語
![](img/lk-miru.gif)
- PDB-1p6w: Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p6w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with the substrate analogue, methyl 4I,4II,4III-tri-thiomaltotetraoside (thio-DP4) | |||||||||
![]() | PROTEIN (Alpha-amylase type A isozyme) | |||||||||
![]() | HYDROLASE / ALPHA-AMYLASE / BARLEY / ISOZYME 1 / BETA-ALPHA-BARREL / SUGAR TONGS BINDING SITE / SUBSTRATE ANALOGUE | |||||||||
Function / homology | ![]() starch catabolic process / alpha-amylase / alpha-amylase activity / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Robert, X. / Haser, R. / Aghajari, N. | |||||||||
![]() | ![]() Title: The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs Authors: Robert, X. / Haser, R. / Gottschalk, T.E. / Ratajczak, F. / Driguez, H. / Svensson, B. / Aghajari, N. #1: ![]() Title: Expression, purification and preliminary crystallographic studies of alpha-amylase isozyme 1 from barley seeds Authors: Robert, X. / Gottschalk, T.E. / Haser, R. / Svensson, B. / Aghajari, N. | |||||||||
History |
| |||||||||
Remark 999 | SEQUENCE According to the authors there is an error in Swissprot database, corrected by the ...SEQUENCE According to the authors there is an error in Swissprot database, corrected by the examination of the crystal structure |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 82.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ht6SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44640.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)- ...beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside Type: oligosaccharide / Mass: 728.800 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||
#3: Polysaccharide | Type: oligosaccharide / Mass: 358.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.42 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PEG 8000, ISOPROPANOL, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 26, 2000 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.6 Å / Num. all: 27556 / Num. obs: 27556 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12.01 Å2 / Rsym value: 0.124 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2→2.11 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.476 / % possible all: 96.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HT6 Resolution: 2→46.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1883521.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.4717 Å2 / ksol: 0.352133 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.52 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|