[English] 日本語
![](img/lk-miru.gif)
- PDB-7ngy: Mycobacterium tuberculosis transcriptional regulator EthR with bo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ngy | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound | ||||||
![]() | HTH-type transcriptional regulator EthR | ||||||
![]() | TRANSCRIPTION / ETHR / Tuberculosis / Inhibition | ||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomlinson, C.W.E. / Tatum, N.J. / Pohl, E. | ||||||
![]() | ![]() Title: Systematic exploration of the hydrophobic capacity of the EthR binding site for lead compound optimization Authors: Tatum, N.J. / Tomlinson, C.W.E. / Frita, R. / Bennett, R. / Baulard, A.R. / Pohl, E. / Kitching, M.O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7ngdC ![]() 7nggC ![]() 7ngiC ![]() 7ngjC ![]() 7ngkC ![]() 7ngmC ![]() 7ngnC ![]() 7ngoC ![]() 7ngrC ![]() 7ngsC ![]() 7ngtC ![]() 7nguC ![]() 7ngwC ![]() 7ngxC ![]() 5nioS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23781.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-UBN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.22 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG based |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→86.05 Å / Num. obs: 67372 / % possible obs: 99.8 % / Redundancy: 17.9 % / CC1/2: 1 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.27→1.29 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3240 / CC1/2: 0.522 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5NIO Resolution: 1.27→60.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.2 Å2 / Biso mean: 24.933 Å2 / Biso min: 9.85 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.27→60.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.27→1.303 Å / Total num. of bins used: 20
|