[English] 日本語
![](img/lk-miru.gif)
- PDB-6py5: Crystal structure of ligand-binding domain of Pseudomonas fluores... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6py5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ligand-binding domain of Pseudomonas fluorescens chemoreceptor CtaA in complex with L-serine | ||||||
![]() | Putative methyl-accepting chemotaxis protein | ||||||
![]() | SIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain | ||||||
Function / homology | ![]() transmembrane signaling receptor activity / chemotaxis / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ud-Din, I.A. / Khan, M.F. / Roujeinikova, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Broad Specificity of Amino Acid Chemoreceptor CtaA ofPseudomonas fluorescensIs Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket. Authors: Ud-Din, A.I.M.S. / Khan, M.F. / Roujeinikova, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 61.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 785.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pxyC ![]() 6py3C ![]() 6py4C ![]() 6pyiC ![]() 6q0fC ![]() 6q0gC ![]() 3c8cS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 27055.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Pf0-1 / Gene: Pfl01_4431 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SER / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 58.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate and Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→33.83 Å / Num. obs: 21256 / % possible obs: 92.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Net I/σ(I): 12.7 / Num. measured all: 79149 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3C8C Resolution: 1.9→33.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.354 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.139 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.47 Å2 / Biso mean: 37.973 Å2 / Biso min: 20.11 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→33.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|