+Open data
-Basic information
Entry | Database: PDB / ID: 3fs0 | ||||||
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Title | Class II ligase ribozyme product-template duplex, structure 2 | ||||||
Components |
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Keywords | RNA / ribozyme / ligase / 2'-5' / 2-5 / 2p5 | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pitt, J.N. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. Authors: Pitt, J.N. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fs0.cif.gz | 21.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fs0.ent.gz | 13.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/3fs0 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/3fs0 | HTTPS FTP |
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-Related structure data
Related structure data | 3ftmSC 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
#1: RNA chain | Mass: 3272.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template strand of Class II ligase A4-11 / References: GenBank: U26406 | ||
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#2: RNA chain | Mass: 3505.170 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Product strand of Class II ligase A4-11, single stranded RNA with one 2'-5' linkage | ||
#3: Chemical | ChemComp-MG / #4: 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: 2.29 Å3/Da / Density % sol: 46.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2mM RNA duplex, 10mM MgCl2, 25% PEG 4000, 0.2M lithium sulfate, 100mM Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 2663 / % possible obs: 99.5 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Num. unique all: 242 / Rsym value: 0.307 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FTM Resolution: 2.3→23.85 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 436790.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→23.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
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Xplor file |
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