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Yorodumi- PDB-2xnz: xpt-pbuX C74U Riboswitch from B. subtilis bound to acetoguanamine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xnz | ||||||
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Title | xpt-pbuX C74U Riboswitch from B. subtilis bound to acetoguanamine identified by virtual screening | ||||||
Components | Guanine riboswitch | ||||||
Keywords | RNA / APTAMER / RNA-LIGAND COMPLEX / MRNA | ||||||
Function / homology | 6-METHYL-1,3,5-TRIAZINE-2,4-DIAMINE / ACETATE ION / : / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Daldrop, P. / Reyes, F.E. / Robinson, D.A. / Hammond, C.M. / Lilley, D.M.J. / Batey, R.T. / Brenk, R. | ||||||
Citation | Journal: Chem. Biol. / Year: 2011 Title: Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Authors: Daldrop, P. / Reyes, F.E. / Robinson, D.A. / Hammond, C.M. / Lilley, D.M. / Batey, R.T. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xnz.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xnz.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xnz ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xnz | HTTPS FTP |
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-Related structure data
Related structure data | 2xnwC 2xo0C 2xo1C 2g9cS 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
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 21507.768 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 15-81 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria) |
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-Non-polymers , 5 types, 230 molecules
#2: Chemical | ChemComp-NCO / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-3AW / | #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 74 C WAS ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 10MM K-HEPES PH 7.5, 12MM COBALT HEXAMMINE, 800MM AMMONIUM ACETATE, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93344 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93344 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→66.08 Å / Num. obs: 25334 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G9C Resolution: 1.59→66.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.947 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 15 AND 81 ARE NOT MODELLED BECAUSE UNORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.438 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→66.08 Å
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Refine LS restraints |
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