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Yorodumi- PDB-5f26: Crystal structures of Pribnow box consensus promoter sequence (P63) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f26 | ||||||
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Title | Crystal structures of Pribnow box consensus promoter sequence (P63) | ||||||
Components |
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Keywords | DNA / Racemic DNA crystallography / Pribnow box / Bacterial Promoter / B-DNA | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Srivastava, S.C. / Huc, I. | ||||||
Funding support | France, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f26.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f26.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/5f26 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/5f26 | HTTPS FTP |
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-Related structure data
Related structure data | 5et9C 5ewbC 5eyqC 5ezfC 5j0eC 463dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Pribnow box consensus sequence TATAAT / 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.62 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: DNA, sodium cacodylate, barium chloride, potassium chloride, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol PH range: 7 |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 11, 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: 2.9→42.64 Å / Num. obs: 2101 / % possible obs: 99.6 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 16.94 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 1.78 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 463D Resolution: 3→36.074 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→36.074 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.0004→36.0771 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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