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- PDB-2ohe: Structural and mutational analysis of tRNA-Intron splicing endonu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ohe | ||||||
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Title | Structural and mutational analysis of tRNA-Intron splicing endonuclease from Thermoplasma acidophilum DSM 1728 | ||||||
![]() | tRNA-splicing endonuclease | ||||||
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Function / homology | ![]() tRNA-type intron splice site recognition and cleavage / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y.K. / Mizutani, K. / Rhee, K.H. / Lee, W.H. / Park, S.Y. / Hwang, K.Y. | ||||||
![]() | ![]() Title: Structural and Mutational Analysis of tRNA Intron-Splicing Endonuclease from Thermoplasma acidophilum DSM 1728: Catalytic Mechanism of tRNA Intron-Splicing Endonucleases Authors: Kim, Y.K. / Mizutani, K. / Rhee, K.H. / Nam, K.H. / Lee, W.H. / Lee, E.H. / Kim, E.E. / Park, S.Y. / Hwang, K.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 54.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: Protein | Mass: 33394.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.68 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 2.4M NaCl, 0.1M Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 12, 2006 / Details: wiggler |
Radiation | Monochromator: wiggler / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→50 Å / Num. obs: 35520 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.066 |
Reflection shell | Resolution: 2.7→2.9 Å / Mean I/σ(I) obs: 4.44 / Num. unique all: 1887 / Rsym value: 0.29 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3258 Å2 / ksol: 0.385537 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→17.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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