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- PDB-1q9a: Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q9a | ||||||
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Title | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | ||||||
![]() | Sarcin/ricin 23S rRNA | ||||||
![]() | RNA / sarcin/ricin domain / ribonucleic acid / RNA recognition / high resolution / ribosomes | ||||||
Function / homology | : / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Correll, C.C. / Beneken, J. / Plantinga, M.J. / Lubbers, M. / Chan, Y.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 8744.255 Da / Num. of mol.: 1 / Fragment: sarcin/ricin domain / Source method: obtained synthetically Details: THE 23S ribosomal RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 23S ribosomal RNA IS NATURALLY FOUND IN Escherichia coli (bacteria). References: GenBank: 26111017 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.57 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, K-MOPS, magnesium chloride, manganese 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: ![]() ![]() ![]() |
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: 1.04→40 Å / Num. all: 31452 / Num. obs: 29848 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 55.3 |
Reflection shell | Resolution: 1.04→1.06 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / % possible all: 82.5 |
Reflection shell | *PLUS % possible obs: 82.5 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.04→40 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.319 |