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- PDB-3b5f: Crystal Structure of a Minimally Hinged Hairpin Ribozyme Incorpor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b5f | ||||||
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Title | Crystal Structure of a Minimally Hinged Hairpin Ribozyme Incorporating the Ade38Dap Mutation and a 2',5' Phosphodiester Linkage at the Active Site | ||||||
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![]() | RNA / hairpin ribozyme / 2 / 6 diaminopurine / 2' / 5' phosphodiester linkage | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | MacElrevey, C. / Krucinska, J. / Wedekind, J.E. | ||||||
![]() | ![]() Title: Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. Authors: MacElrevey, C. / Salter, J.D. / Krucinska, J. / Wedekind, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.8 KB | Display | ![]() |
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PDB format | ![]() | 32.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.7 KB | Display | ![]() |
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Full document | ![]() | 430.7 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b58C ![]() 3b5aC ![]() 3b5sC ![]() 3b91C ![]() 3bbiC ![]() 3bbkC ![]() 3bbmC ![]() 3cr1C ![]() 2p7fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase synthesis at Keck Institute, Yale / References: ![]() | ||
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#2: RNA chain | Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: solid phase chemical synthesis at Dharmacon, Colorado References: ![]() | ||
#3: RNA chain | Mass: 6006.583 Da / Num. of mol.: 1 / Mutation: A38(N6G), U39C / Source method: obtained synthetically Details: solid phase chemical synthesis at Dharmacon, Colorado References: ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 78 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 6.8, 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2007 Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING |
Radiation | Monochromator: horizontal bent Si(111) asymmetrically cut w/ water cooled Cu block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40.48 Å / Num. all: 10109 / Num. obs: 9960 / % possible obs: 99.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 79.6 Å2 / Rsym value: 0.05 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 962 / Rsym value: 0.459 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2P7F Resolution: 2.7→38.32 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 599805.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 Details: Alternate conformation at U1 of chain A. S9L and N6G are covalently attached to ribozyme
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→38.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.97 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 4
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Xplor file |
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