[English] 日本語
![](img/lk-miru.gif)
- PDB-6hlx: Structure of the PBP AgaA in complex with agropinic acid from A.t... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6hlx | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10 | ||||||
![]() | AgaA | ||||||
![]() | TRANSPORT PROTEIN / periplasmic binding protein / ABC transporter | ||||||
Function / homology | ![]() ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Marty, L. / Vigouroux, A. | ||||||
![]() | ![]() Title: Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogenAgrobacterium tumefaciens. Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Pelissier, F. / Meyer, T. / Lavire, C. / Dessaux, Y. / Morera, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 221.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 172.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 894.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 896.7 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hlyC ![]() 6hlzC ![]() 6hm2C ![]() 1dppS ![]() 3f1qS 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: 54459.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 9 types, 507 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/G9Z.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/G9Z.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-G9Z / | #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PEG / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.25 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 1.8 M AS, 0.1 M Mes pH 6.5, 0.2 M Zn acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→52.48 Å / Num. obs: 82437 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 26.82 Å2 / Rsym value: 0.132 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Rsym value: 2.052 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3F1Q and 1DPP Resolution: 1.65→52.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.067
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→52.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.66 Å / Total num. of bins used: 50
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 80.1144 Å / Origin y: -31.7036 Å / Origin z: 1.2197 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|25 - A|169 A|175 - A|315 A|322 - A|512 } |