[English] 日本語
![](img/lk-miru.gif)
- PDB-6j33: Crystal structure of ligand-free of PulA from Klebsiella pneumoniae -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6j33 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ligand-free of PulA from Klebsiella pneumoniae | ||||||
![]() | pullulanase | ||||||
![]() | HYDROLASE / Pullulanase / Klebsiella pneumoniae / ligand-free / G680 | ||||||
Function / homology | ![]() pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saka, N. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase. Authors: Saka, N. / Malle, D. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1005 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 826.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 478.1 KB | Display | |
Data in XML | ![]() | 103 KB | Display | |
Data in CIF | ![]() | 165 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j34C ![]() 6j35C ![]() 6j4hC ![]() 2fhfS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 114462.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | N229S was due to spontaneous mutation. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium acetate, 0.2M Sodium Acetate buffer (pH 6.0), 20%(w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.297→50 Å / Num. obs: 495665 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Net I/av σ(I): 0.201 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.3→1.34 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 46251 / CC1/2: 0.849 / Rpim(I) all: 0.24 / Rrim(I) all: 0.413 / % possible all: 88 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2FHF Resolution: 1.297→39.264 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.53 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.297→39.264 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|