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Yorodumi- PDB-2d2k: Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d2k | ||||||
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Title | Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme | ||||||
Components |
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Keywords | RNA / ribozyme / S-turn / dual conformation | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.65 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 | 2d2k.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d2k.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 2d2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d2k_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 2d2k_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 2d2k_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 2d2k_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2k ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2k | HTTPS FTP |
-Related structure data
Related structure data | 1x9cSC 1x9kC 2d2lC 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: 5992.552 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: 4.2 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: Mar 17, 2005 / Details: confocal |
Radiation | Monochromator: Osmic Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→34.01 Å / Num. all: 9930 / Num. obs: 9889 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 93.6 Å2 / Rsym value: 0.07 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 7.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1X9C Resolution: 2.65→34.01 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1611786.47 / 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: 174.738 Å2 / ksol: 0.446011 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→34.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.92 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 4
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Xplor file |
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