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Yorodumi- PDB-1q96: Crystal structure of a mutant of the sarcin/ricin domain from rat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q96 | ||||||
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Title | Crystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA | ||||||
Components | sarcin/ricin 28S rRNA | ||||||
Keywords | RNA / sarcin/ricin domain / ribonucleic acid / RNA recognition / ribosomes / elongation factors / mutant / stem loop | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Correll, C.C. / Beneken, J. / Plantinga, M.J. / Lubbers, M. / Chan, Y.L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2003 Title: The common and distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure Authors: Correll, C.C. / Beneken, J. / Plantinga, M.J. / Lubbers, M. / Chan, Y.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q96.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q96.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q96 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q96 | HTTPS FTP |
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-Related structure data
Related structure data | 1q93C 1q9aC 483dS 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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2 |
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3 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 8711.271 Da / Num. of mol.: 3 / Fragment: sarcin/ricin domain / Mutation: C13U, G18A / Source method: obtained synthetically Details: THE 28S ribosomal RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 28S ribosomal RNA IS NATURALLY FOUND IN Rattus rattus (RAT). References: GenBank: 3891767 #2: Chemical | ChemComp-SO4 / #3: 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: 2.88 Å3/Da / Density % sol: 57.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, K-MOPS, magnesium chloride, spermine, cobalt chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97764 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97764 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 32531 / Num. obs: 29876 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2 / % possible all: 80 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 91.3 % |
Reflection shell | *PLUS % possible obs: 80 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 483D Resolution: 1.75→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.294 / Rfactor Rwork: 0.269 |