+Open data
-Basic information
Entry | Database: PDB / ID: 2g32 | ||||||
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Title | Crystal structure of an RNA racemate | ||||||
Components |
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Keywords | RNA / double helix / racemate | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Rypniewski, W. / Vallazza, M. / Perbandt, M. / Klussmann, S. / Betzel, C. / Erdmann, V.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: The first crystal structure of an RNA racemate. Authors: Rypniewski, W. / Vallazza, M. / Perbandt, M. / Klussmann, S. / Delucas, L.J. / Betzel, C. / Erdmann, V.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g32.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g32.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 2g32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g32 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g32 | HTTPS FTP |
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-Related structure data
Related structure data | 2gpmC 2gq4C 2gq5C 2gq6C 2gq7C 1r3oS 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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2 |
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Unit cell |
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Number of models | 2 |
-Components
#1: RNA chain | Mass: 2597.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) #2: RNA chain | Mass: 2517.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 1.96 Å3/Da / Density % sol: 37.21 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 7% PEG 400, 0.1 M CaCl2, 50mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2003 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.801 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. all: 37262 / Num. obs: 37262 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.056 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / Num. unique all: 1835 / Rsym value: 0.52 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1r3o Resolution: 1.3→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a obs: 0.0324 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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