+
Open data
-
Basic information
Entry | Database: PDB / ID: 4hqm | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of QsrR-menadione complex | ||||||
![]() | QsrR protein | ||||||
![]() | TRANSCRIPTION regulator / menadione-modified protein / DNA | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / 2-methylnaphthalene-1,4-diol / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. ...Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C. | ||||||
![]() | ![]() Title: Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Authors: Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Cho, H. / Brugarolas, P. / Gao, Y.N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 49.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13071.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | Sequence details | THE AUTHOR STATES THAT THE RESIDUES AT POSITIONS 30 AND 33 ARE CONSISTENT | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M NaCl, 0.1 M Tris.HCl, pH 8.5, 25% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 8886 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.476 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→19.405 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|