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Yorodumi- PDB-2a43: Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a43 | ||||||
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Title | Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif | ||||||
Components | RNA Pseudoknot | ||||||
Keywords | RNA / PLRV / potato leaf roll virus / BWYV / beet western yellow virus / pk / pseudoknot / RNA. | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Pallan, P.S. / Marshall, W.S. / Harp, J. / Jewett III, F.C. / Wawrzak, Z. / Brown II, B.A. / Rich, A. / Egli, M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif Authors: Pallan, P.S. / Marshall, W.S. / Harp, J. / Jewett III, F.C. / Wawrzak, Z. / Brown II, B.A. / Rich, A. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a43.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a43.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a43_validation.pdf.gz | 388.4 KB | Display | wwPDB validaton report |
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Full document | 2a43_full_validation.pdf.gz | 391.8 KB | Display | |
Data in XML | 2a43_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 2a43_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a43 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a43 | HTTPS FTP |
-Related structure data
Related structure data | 437dS 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 on special symmetry positions |
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Details | One RNA pseudoknot per asymmetric unit |
-Components
#1: RNA chain | Mass: 8340.073 Da / Num. of mol.: 1 / Mutation: C17U, A18C / Source method: obtained synthetically Details: Chemically synthesized oligonucleotide (RNA). This sequence is a mutated form of that naturally found in Potato leafroll virus References: GenBank: 23953793 | ||
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#2: Chemical | #3: 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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, Magnesium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9198 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2003 / Details: Horizontally focusing mirrors |
Radiation | Monochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→23.6 Å / Num. obs: 19756 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.58 |
Reflection shell | Resolution: 1.34→1.4 Å / Redundancy: 7.64 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.97 / Num. unique all: 1748 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 437D Resolution: 1.34→23.6 Å / Cross valid method: THROUGHOUT / σ(F): 4 Stereochemistry target values: G. Parkinson et. al., Acta Cryst. (1996) D52, 57-64. Details: The waters 603, 686, 211, 584, 610, 666, 608 and 638 have partial occupancies. Thus close contacts between them should be ignored.
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Refinement step | Cycle: LAST / Resolution: 1.34→23.6 Å
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Refine LS restraints |
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