[English] 日本語
![](img/lk-miru.gif)
- PDB-6rkl: The crystal structure of AbnE, an arabino-oligosaccharide binding... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rkl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinoheptaose | |||||||||
![]() | Arabino-oligosaccharids-binding protein | |||||||||
![]() | SUGAR BINDING PROTEIN / Geobacillus stearothermophilus / ABC transporter / arabino-oligosaccharide / arabinohexaose | |||||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Arabino-oligosaccharids-binding protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lansky, S. / Salama, R. / Shoham, Y. / Shoham, G. | |||||||||
![]() | ![]() Title: Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. Authors: Lansky, S. / Salama, R. / Shulami, S. / Lavid, N. / Sen, S. / Schapiro, I. / Shoham, Y. / Shoham, G. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 114.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 708.2 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rjyC ![]() 6rkhSC ![]() 6rkjC ![]() 6rkxC ![]() 6rl1C ![]() 6rl2C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 48689.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: abnE / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22% PEG 4K, 0.1M Tris/HCl buffer, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 35228 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / Num. unique obs: 4737 / % possible all: 95.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6RKH Resolution: 2→28.625 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.59
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.625 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|