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- PDB-2dr5: Complex structure of CCA adding enzyme with mini-helix lacking CCA -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dr5 | ||||||
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Title | Complex structure of CCA adding enzyme with mini-helix lacking CCA | ||||||
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![]() | TRANSFERASE/RNA / protein-rna complex / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | ![]() CCA tRNA nucleotidyltransferase / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomita, K. / Ishitani, R. / Fukai, S. / Nureki, O. | ||||||
![]() | ![]() Title: Complete crystallographic analysis of the dynamics of CCA sequence addition Authors: Tomita, K. / Ishitani, R. / Fukai, S. / Nureki, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.7 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2dr7C ![]() 2dr8C ![]() 2dr9C ![]() 2draC ![]() 2drbC ![]() 2dviC ![]() 1uetS 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
#1: RNA chain | Mass: 10294.140 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 51469.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.26 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 50mM HEPES, 20% PEG 3550, 0.2M Tri-lithium citrate, 80mM NH4SO4, pH 7.5, VAPOR DIFFUSION, 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 315 / Detector: CCD / Date: May 17, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 19376 / Num. obs: 19376 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 80 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UET Resolution: 2.8→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2888737.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.280021 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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