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- PDB-359d: INHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 359d | ||||||
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Title | INHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-SPECIFIC BINDING OF TB(III) | ||||||
![]() | (RNA HAMMERHEAD RIBOZYME) x 2 | ||||||
![]() | RIBOZYME / RNA HAMMERHEAD RIBOZYME / CATALYTIC RNA / LOOP | ||||||
Function / homology | TERBIUM(III) ION / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Feig, A.L. / Scott, W.G. / Uhlenbeck, O.C. | ||||||
![]() | ![]() Title: Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb. Authors: Feig, A.L. / Scott, W.G. / Uhlenbeck, O.C. #1: ![]() Title: Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme Authors: Scott, W.G. / Murray, J.B. / Arnold, J.R.P. / Stoddard, B.L. / Klug, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.4 KB | Display | ![]() |
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Full document | ![]() | 401.1 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 299dS S: Starting model for refinement |
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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: 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-TB / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.49 Å3/Da / Density % sol: 78 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: unknown / Details: Scott, W.G., (1996) Science, 274, 2065. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→35.8 Å / Num. obs: 7810 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Rsym value: 0.047 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.079 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 35.8 Å / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Num. measured all: 30459 |
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Processing
Software |
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Refinement | Starting model: NDB ENTRY URX057 (PDB ENTRY 299D) Resolution: 2.9→35.8 Å / σ(F): 0 Details: BULK SOLVENT MODEL EMPLOYED TO INCLUDE ALL LOW RESOLUTION DATA
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Displacement parameters | Biso mean: 52.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→35.8 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 35.8 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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