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Yorodumi- PDB-1a79: CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a79 | ||||||
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Title | CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII | ||||||
Components | TRNA ENDONUCLEASE | ||||||
Keywords | ENDONUCLEASE / TRNA ENDONUCLEASE | ||||||
Function / homology | Function and homology information tRNA-type intron splice site recognition and cleavage / tRNA-intron lyase / tRNA-intron endonuclease activity / nucleic acid binding / lyase activity Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å | ||||||
Authors | Li, H. / Trotta, C.R. / Abelson, J.N. | ||||||
Citation | Journal: Science / Year: 1998 Title: Crystal structure and evolution of a transfer RNA splicing enzyme. Authors: Li, H. / Trotta, C.R. / Abelson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a79.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a79.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a79 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a79 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 19745.783 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): BLR (DE3) / References: UniProt: Q58819 #2: Chemical | #3: Chemical | ChemComp-AU / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion / PH range low: 6 / PH range high: 5.5 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.02 / Wavelength: 1.02, 1.54 | |||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Sep 7, 1997 | |||||||||
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→100 Å / Num. obs: 75778 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 10.3 | |||||||||
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.167 / % possible all: 65.4 | |||||||||
Reflection | *PLUS Num. measured all: 165549 | |||||||||
Reflection shell | *PLUS % possible obs: 65.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.28→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.28→2.36 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.857 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.302 |