[English] 日本語
![](img/lk-miru.gif)
- PDB-4ra1: PBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ra1 | ||||||
---|---|---|---|---|---|---|---|
Title | PBP AccA from A. tumefaciens C58 in complex with D-Glucose-2-phosphate | ||||||
![]() | ABC transporter, substrate binding protein (Agrocinopines A and B) | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic binding protein C cluster | ||||||
Function / homology | ![]() dipeptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | El Sahili, A. / Morera, S. | ||||||
![]() | ![]() Title: A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. Authors: El Sahili, A. / Li, S.Z. / Lang, J. / Virus, C. / Planamente, S. / Ahmar, M. / Guimaraes, B.G. / Aumont-Nicaise, M. / Vigouroux, A. / Soulere, L. / Reader, J. / Queneau, Y. / Faure, D. / Morera, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 219.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 172.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ze8C ![]() 4ze9C ![]() 4zebC ![]() 4zecC ![]() 4zedC ![]() 4zeiC ![]() 4zekC ![]() 4oux ![]() 4oup ![]() 4out ![]() 4ouv ![]() 4ouw ![]() 4ouy ![]() 4ouz S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57178.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Sugars , 2 types, 2 molecules ![](data/chem/img/ALX.gif)
![](data/chem/img/BNX.gif)
![](data/chem/img/BNX.gif)
#2: Sugar | ChemComp-ALX / |
---|---|
#3: Sugar | ChemComp-BNX / |
-Non-polymers , 3 types, 386 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | ALX AND BNX ARE IN ALTERNATE CONFORMATI |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4K, 0.2M NH4 Acetate, 0.1M NaCitrate, pH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 51001 / Num. obs: 50794 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.73 Å2 |
Reflection shell | Resolution: 1.75→1.85 Å / % possible all: 97.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4OUX ![]() 4oux Resolution: 1.75→42.45 Å / Cor.coef. Fo:Fc: 0.9422 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→42.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -16.5991 Å / Origin y: -26.3669 Å / Origin z: 14.5518 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|32 - A|521 } |