[English] 日本語
![](img/lk-miru.gif)
- PDB-5ot8: Structure of the periplasmic binding protein (PBP) NocT-G97S muta... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ot8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the periplasmic binding protein (PBP) NocT-G97S mutant from A. tumefaciens C58 in complex with octopine. | ||||||
![]() | Nopaline-binding periplasmic protein | ||||||
![]() | PROTEIN BINDING / Agrobacterium tumefaciens / Arginine / Bacterial Proteins / DNA / Bacterial / Gene Expression Regulation / Genes / Ligands / Plant Tumors / Plasmids | ||||||
Function / homology | ![]() nitrogen compound transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vigouroux, A. / Morera, S. | ||||||
![]() | ![]() Title: Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens. Authors: Vigouroux, A. / El Sahili, A. / Lang, J. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 211.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 168.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 485.1 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oreC ![]() 5orgC ![]() 5ot9C ![]() 5otaC ![]() 5otcC ![]() 5itpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29289.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HHHHHH : Tag Source: (gene. exp.) ![]() Gene: nocT, Atu6027, AGR_pTi_67 / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 67 molecules ![](data/chem/img/6DB.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 0.1 M Tris pH8, 0.1 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 23735 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 57.87 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.35→2.49 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 3814 / Rsym value: 0.715 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ITP Resolution: 2.35→26.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0.001 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.198
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.35→26.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|