+Open data
-Basic information
Entry | Database: PDB / ID: 3d0x | ||||||
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Title | Crystal Structure of the unbound lysine riboswitch | ||||||
Components | RNA (161-MER) | ||||||
Keywords | RNA / riboswitch | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Authors | Batey, R.T. / Garst, A.D. / Heroux, A. / Rambo, R.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structure of the lysine riboswitch regulatory mRNA element. Authors: Garst, A.D. / Heroux, A. / Rambo, R.P. / Batey, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d0x.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d0x.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d0x_validation.pdf.gz | 395.9 KB | Display | wwPDB validaton report |
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Full document | 3d0x_full_validation.pdf.gz | 402.2 KB | Display | |
Data in XML | 3d0x_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 3d0x_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/3d0x ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0x | HTTPS FTP |
-Related structure data
Related structure data | 3d0uSC S: Starting model for refinement C: citing same article (ref.) |
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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: RNA chain | Mass: 52465.289 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: LITHIUM SULFATE, MAGNESIUM CHLORIDE, IRIDIUM HEXAMMINE, SODIUM HEPES | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2008 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→19.7 Å / Num. obs: 19610 / % possible obs: 99.4 % / Redundancy: 3.62 % / Biso Wilson estimate: 55.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3D0U without lysine Resolution: 2.95→17.112 Å / SU ML: 0.42 / Phase error: 23.39 / 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 / Bsol: 8.987 Å2 / ksol: 0.208 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→17.112 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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