[English] 日本語
Yorodumi- PDB-5ezf: Racemic crystal structures of Pribnow box consensus promoter sequ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ezf | ||||||
---|---|---|---|---|---|---|---|
Title | Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca) | ||||||
Components |
| ||||||
Keywords | DNA / Pribnow box consensus sequence / -10 element / transcription initiation / B-DNA double helix / DNA double helix | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Srivastava, S.C. / Huc, I. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 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: Journal: Angew. Chem. Int. Ed. / Year: 2014 Title: Racemic DNA Crystallography Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ezf.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ezf.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 5ezf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ezf ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ezf | HTTPS FTP |
---|
-Related structure data
Related structure data | 5et9C 5ewbC 5eyqC 5f26C 5j0eC 1fq2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
---|---|---|---|
#2: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * For crystallization, we used four strands 1) d(CGCTATAATGCG) with L-sugars 2) d(CGCATTATAGCG) with L-sugars and 3) d(CGCTATAATGCG) ...Details: Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * For crystallization, we used four strands 1) d(CGCTATAATGCG) with L-sugars 2) d(CGCATTATAGCG) with L-sugars and 3) d(CGCTATAATGCG) with D-sugars 4) d(CGCATTATAGCG) with D-sugars Enantio-pure DNA solutions were prepared first by de-naturation followed by slow cooling down process to ensure proper folding of the hetero-duplex formed between the non-self complementary strands. After slow-annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic DNA mixture was used for crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→32.86 Å / Num. obs: 12549 / % possible obs: 99.86 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 16.92 |
Reflection shell | Resolution: 1.65→1.79 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.75 / % possible all: 99.76 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FQ2 Resolution: 1.65→32.856 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→32.856 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|