[English] 日本語
![](img/lk-miru.gif)
- PDB-6a8s: Crystal Structure of the putative amino acid-binding periplasmic ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6a8s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine | ||||||
![]() | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
![]() | TRANSPORT PROTEIN / Candidatus Liberibacter asiaticus / Periplasmic / Solute Binding / Cysteine | ||||||
Function / homology | ![]() | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Kesari, P. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
![]() | ![]() Title: Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding. Authors: Kumar, P. / Kesari, P. / Kokane, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 118.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6a80C ![]() 6aa1C ![]() 6aalC ![]() 2ylnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27615.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: psy62 / Gene: CLIBASIA_05070 / Plasmid: pET28C / Production host: ![]() ![]() |
---|
-Non-polymers , 7 types, 208 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % / Description: Cubic |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2M Ammonium sulphate, 0.1M Sodium acetate Trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→70.89 Å / Num. obs: 31433 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.071 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3028 / CC1/2: 0.702 / Rpim(I) all: 0.452 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2YLN Resolution: 2.05→36.885 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.71 / 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: 2.05→36.885 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|