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Yorodumi- PDB-2d2l: Crystal Structure of a minimal, all-RNA hairpin ribozyme with a p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d2l | |||||||||
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Title | Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 | |||||||||
Components |
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Keywords | RNA / ribozyme / propyl linker | |||||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | |||||||||
Authors | Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme Authors: Grum-Tokars, V. / Milovanovic, M. / Wedekind, J.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d2l.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d2l.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2l ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2l | HTTPS FTP |
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-Related structure data
Related structure data | 1x9cSC 1x9kC 2d2kC 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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Unit cell |
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-Components
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: RNA chain | Mass: 5824.445 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 12 molecules
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #7: 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: 4.1 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2005 / Details: Confocal Osmic |
Radiation | Monochromator: Confocal Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30.7 Å / Num. all: 11412 / Num. obs: 11302 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 7 / Rsym value: 0.42 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1X9C Resolution: 2.5→30.67 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1344888.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS v1.1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 88.2321 Å2 / ksol: 0.408215 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.75 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 4
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Xplor file |
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