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- PDB-3if0: Crystal Structure of the Nanoarchaeum equitans tRNA splicing endo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3if0 | ||||||
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Title | Crystal Structure of the Nanoarchaeum equitans tRNA splicing endonuclease structural subunit | ||||||
![]() | NEQ261 | ||||||
![]() | HYDROLASE / protein | ||||||
Function / homology | ![]() tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mitchell, M. / Li, H. | ||||||
![]() | ![]() Title: Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Authors: Mitchell, M. / Xue, S. / Erdman, R. / Randau, L. / Soll, D. / Li, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.3 KB | Display | ![]() |
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PDB format | ![]() | 30.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 436.3 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ieySC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18448.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.88 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.10 M sodium acetate pH 4.6, 0.30 M ammonium acetate, 35% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. all: 13062 / Num. obs: 13062 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 8 / Redundancy: 19 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.624 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3IEY Resolution: 2.2→41.38 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.168 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.247 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.6367 Å / Origin y: -21.9329 Å / Origin z: 6.3322 Å
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