[English] 日本語
![](img/lk-miru.gif)
- PDB-5j0e: Crystal structures of Pribnow box consensus promoter sequence (P32) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5j0e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of Pribnow box consensus promoter sequence (P32) | ||||||
![]() |
| ||||||
![]() | DNA / Pribnow box / consensus promoter-sequence / Racemic DNA / DNA crystallography | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. Authors: Mandal, P.K. / Collie, G.W. / Srivastava, S.C. / Kauffmann, B. / Huc, I. #1: ![]() Title: Racemic DNA Crstallography Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 49.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 408.6 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5et9C ![]() 5ewbC ![]() 5eyqC ![]() 5ezfC ![]() 5f26C ![]() 463dS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: This dodecanucleotide sequence contains the Pribnow box consensus promoter sequence TATAAT at the centre Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 3702.428 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, sodium cacodylate, zinc chloride, spermine |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 1, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 2.81→40.62 Å / Num. obs: 5955 / % possible obs: 99.3 % / Redundancy: 1.98 % / Rmerge(I) obs: 0.0283 / Rsym value: 0.0369 / Net I/σ(I): 17.08 | |||||||||||||||
Reflection shell | Resolution: 2.81→2.91 Å / Redundancy: 1.91 % / Rmerge(I) obs: 0.1357 / Mean I/σ(I) obs: 3.87 / % possible all: 96.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 463D Resolution: 2.81→40.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.066 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.455 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.81→40.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|