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Yorodumi- PDB-4g6p: Minimal Hairpin Ribozyme in the Precatalytic State with A38P Variation -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g6p | ||||||
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Title | Minimal Hairpin Ribozyme in the Precatalytic State with A38P Variation | ||||||
Components |
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Keywords | RNA / Structure-activity relationship / Nucleic Acid Conformation | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.641 Å | ||||||
Authors | Liberman, J.A. / Jenkins, J.L. / Krucinska, J. / Wedekind, J.E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis. Authors: Liberman, J.A. / Guo, M. / Jenkins, J.L. / Krucinska, J. / Chen, Y. / Carey, P.R. / 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 | 4g6p.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g6p.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 4g6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/4g6p ftp://data.pdbj.org/pub/pdb/validation_reports/g6/4g6p | HTTPS FTP |
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-Related 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 , 3 types, 3 molecules ABC
#1: RNA chain | Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 5976.554 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 6 molecules
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | #6: 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: 4.29 Å3/Da / Density % sol: 71.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% (w/v) PEG 2000 MME, 0.1M HEPES pH=7.0, 0.25 M Lithium Sulfate, 1mM Cobalt Hexamine, 2mM spermadine, vapor diffusion, Hanging Drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97885 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 5, 2010 / Details: Rh coated flat mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97885 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→50 Å / Num. obs: 10642 / % possible obs: 98.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.043 / Χ2: 1.27 / Net I/σ(I): 20.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.641→31.017 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.4 / σ(F): 0 / Phase error: 25.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.527 Å2 / ksol: 0.295 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.54 Å2 / Biso mean: 77.9394 Å2 / Biso min: 56.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.641→31.017 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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