+Open data
-Basic information
Entry | Database: PDB / ID: 1x9c | ||||||
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Title | An all-RNA Hairpin Ribozyme with mutation U39C | ||||||
Components |
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Keywords | RNA / Hairpin ribozyme / all-RNA / cobalt hexaamine / mutation / junctionless / low salt / S-turn / E-loop / catalytic RNA / 2'-OMe | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 | 1x9c.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x9c.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x9c ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x9c | HTTPS FTP |
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-Related structure data
Related structure data | 1x9kC 2d2kC 2d2lC 1m5kS 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 on special symmetry positions |
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-Components
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4066.497 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically / Details: Solid Phase Chemical Synthesis |
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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: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 45 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: 69.5 % | ||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2004 |
Radiation | Monochromator: Bent triangular asymmetric cut Si(111) monochromater (provides horizontal foc ussing); Rh-coated Si mirror for vertical focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→25 Å / Num. all: 17374 / Num. obs: 17084 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.01 % / Biso Wilson estimate: 76.8 Å2 / Rsym value: 0.036 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 5.61 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 1684 / Rsym value: 0.371 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1M5K Resolution: 2.19→24.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1314456.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 Stereochemistry target values: Parkinson et al. (1996) Acta Cryst. D52, 57-64
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.6987 Å2 / ksol: 0.304022 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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