[English] 日本語
![](img/lk-miru.gif)
- PDB-1mxd: Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperther... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1mxd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei | |||||||||
![]() | alpha amylase | |||||||||
![]() | HYDROLASE / (beta/alpha)8-barrel / alpha-amylase / family 13 glycosyl hydrolase | |||||||||
Function / homology | ![]() alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Linden, A. / Mayans, O. / Meyer-Klaucke, W. / Antranikian, G. / Wilmanns, M. | |||||||||
![]() | ![]() Title: Differential Regulation of a Hyperthermophilic alpha-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc Authors: Linden, A. / Mayans, O. / Meyer-Klaucke, W. / Antranikian, G. / Wilmanns, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mwoSC ![]() 1mxgC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50228.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O08452, UniProt: Q7LYT7*PLUS, alpha-amylase |
---|
-Sugars , 2 types, 5 molecules ![](data/chem/img/GLC.gif)
#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose #5: Sugar | ChemComp-GLC / | |
---|
-Non-polymers , 4 types, 297 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, MPD, zinc acetate, acarbose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 2000 / Details: Premirror, Bent mirror |
Radiation | Monochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8453 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→20 Å / Num. all: 35302 / Num. obs: 35302 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.97→2 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1619 / % possible all: 88.1 |
Reflection | *PLUS Lowest resolution: 99 Å |
Reflection shell | *PLUS Lowest resolution: 2.02 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.32 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1MWO Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.219 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |