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Yorodumi- PDB-300d: CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 300d | ||||||
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Title | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMMERHEAD RIBOZYME, MN(II)-SOAKED | ||||||
Components | (RNA HAMMERHEAD RIBOZYME) x 2 | ||||||
Keywords | RIBOZYME / RNA HAMMERHEAD RIBOZYME / CATALYTIC RNA / LOOP | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Scott, W.G. / Murray, J.B. / Arnold, J.R.P. / Stoddard, B.L. / Klug, A. | ||||||
Citation | Journal: Science / Year: 1996 Title: Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Authors: Scott, W.G. / Murray, J.B. / Arnold, J.R. / Stoddard, B.L. / Klug, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 300d.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb300d.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 300d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/00/300d ftp://data.pdbj.org/pub/pdb/validation_reports/00/300d | 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
#1: RNA chain | Mass: 5170.103 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 8019.876 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-MN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.2 Å3/Da / Density % sol: 80.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: MARRESEARCH / Date: Sep 28, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→43 Å / Num. obs: 6716 / % possible obs: 93.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.5 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 43 Å / % possible obs: 93.6 % |
-Processing
Software |
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Refinement | Resolution: 3→8 Å / σ(F): 2 Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
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Refine Biso | Class: ALL ATOMS / Details: TR / Treatment: isotropic | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: NDB_PARAMETER_FILE.RNA / Topol file: NDB_TOPOLOGY_FILE.RNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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