+Open data
-Basic information
Entry | Database: PDB / ID: 2ees | ||||||
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Title | Guanine riboswitch A21U, U75A mutant bound to hypoxanthine | ||||||
Components | Guanine riboswitch | ||||||
Keywords | RNA / mRNA / riboswitch / guanine / hypoxanthine / RNA-ligand complex / double helix / three-way junction | ||||||
Function / homology | ACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Gilbert, S.D. / Edwards, A.L. / Batey, R.T. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Mutational analysis of the purine riboswitch aptamer domain Authors: Gilbert, S.D. / Love, C.E. / Edwards, A.L. / Batey, R.T. | ||||||
History |
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Remark 999 | SEQUENCE Residues U21 and A75 were engineered from A and U, respectively, based on the guanine ...SEQUENCE Residues U21 and A75 were engineered from A and U, respectively, based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ees.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ees.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ees.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ees_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 2ees_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 2ees_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2ees_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2ees ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2ees | HTTPS FTP |
-Related structure data
Related structure data | 2eetC 2eeuC 2eevC 2eewC 1u8d 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: RNA chain | Mass: 21506.783 Da / Num. of mol.: 1 / Mutation: A21U, U75A / Source method: obtained synthetically Details: This sequence was engineered based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis(bacteria). References: PDB-PDB | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | ChemComp-NCO / #4: Chemical | ChemComp-HPA / | #5: 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: 2.3 Å3/Da / Density % sol: 46.45 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% Polyethylene glycol 3000, 640mM ammonium acetate, 10mM cobalt hexammine chloride, 10mM K(+)-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 22, 2006 |
Radiation | Monochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 19460 / Num. obs: 19129 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.42 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.81 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1917 / Rsym value: 0.17 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U8D 1u8d Resolution: 1.75→19.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1061848.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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