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- PDB-5eaq: Two active site divalent ion in the crystal structure of the hamm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eaq | ||||||
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Title | Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+ | ||||||
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![]() | RNA / ribozyme / hammerhead | ||||||
Function / homology | : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mir, A. / Golden, B.L. | ||||||
![]() | ![]() Title: Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue. Authors: Mir, A. / Golden, B.L. #1: ![]() Title: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. Authors: Mir, A. / Chen, J. / Robinson, K. / Lendy, E. / Goodman, J. / Neau, D. / Golden, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eaoC ![]() 5di2S C: citing same article ( 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 on special symmetry positions |
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Components
#1: RNA chain | Mass: 15500.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pUC19 / Production host: ![]() ![]() |
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#2: RNA chain | Mass: 6536.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-MN / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.07 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 50 mM Tris pH 8.2, 10 mM MgCl2, 32% MPD, 0.9 M KCl, 0.5 mM spermine 2 mM NH4VO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.501 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 12773 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 139.7 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 19.4 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DI2 Resolution: 3.201→27.429 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.201→27.429 Å
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Refine LS restraints |
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LS refinement shell |
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