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- PDB-5eyq: Racemic crystal structures of Pribnow box consensus promoter sequ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eyq | ||||||
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Title | Racemic crystal structures of Pribnow box consensus promoter sequence (Pnna) | ||||||
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![]() | DNA / Pribnow box consensus sequence / -10 element / transcription initiation / B-DNA double helix | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Srivastava, S.C. / Huc, I. | ||||||
Funding support | ![]()
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![]() | ![]() 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 Crystallography Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.8 KB | Display | ![]() |
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PDB format | ![]() | 15.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 344.2 KB | Display | ![]() |
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Full document | ![]() | 348.2 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5et9C ![]() 5ewbC ![]() 5ezfC ![]() 5f26C ![]() 5j0eC ![]() 1bnaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD *For crystallization, we used four strands (1) d(CGCTATAATGCG) with L-sugars ...Details: Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD *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 L-DNA solution (strands 1,2) and D-DNA solution (strands 3,4) were prepared first with denaturation followed by slow annealing process to ensure proper folding of the duplex formed between the non-self complementary strands. After annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization. |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.23 Å / Num. obs: 2825 / % possible obs: 96.61 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 1.34 / % possible all: 78.57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNA Resolution: 2.3→34.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.534 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 37.461 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→34.23 Å
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Refine LS restraints |
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