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- PDB-6dn2: CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dn2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA | ||||||
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![]() | RNA / FMN / RIBOSWITCH / TRANSCRIPTION | ||||||
Function / homology | Chem-GZG / : / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. ...Vicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. / Suto, R.K. / Coish, P. / Blount, K.F. / Batey, R.T. | ||||||
![]() | ![]() Title: Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. Authors: Vicens, Q. / Mondragon, E. / Reyes, F.E. / Coish, P. / Aristoff, P. / Berman, J. / Kaur, H. / Kells, K.W. / Wickens, P. / Wilson, J. / Gadwood, R.C. / Schostarez, H.J. / Suto, R.K. / Blount, K.F. / Batey, R.T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.8 KB | Display | ![]() |
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Full document | ![]() | 737.7 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dn1C ![]() 6dn3C ![]() 3f4eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain , 2 types, 2 molecules XY
#1: RNA chain | Mass: 17455.389 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: IN VITRO TRANSCRIBED RNA FROM FUSOBACTERIUM NUCLEATUM IMPX GENE Source: (synth.) ![]() |
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#2: RNA chain | Mass: 18092.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 17 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GZG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GZG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GZG / | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation / pH: 6.5 / Details: PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 31, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 8864 / % possible obs: 83.4 % / Observed criterion σ(I): 0.5 / Redundancy: 7.1 % / Biso Wilson estimate: 16.83 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.14 |
Reflection shell | Resolution: 2.8→3.23 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.52 / % possible all: 54.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3F4E Resolution: 2.88→19.55 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.854 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.433
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Displacement parameters | Biso max: 190.88 Å2 / Biso mean: 76.52 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.88→19.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.88→3.22 Å / Total num. of bins used: 5
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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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