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Yorodumi- PDB-2csx: Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2csx | ||||||
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Title | Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(Met) | ||||||
Components |
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Keywords | Ligase/RNA / Ligase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / Ligase-RNA COMPLEX | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Nakanishi, K. / Ogiso, Y. / Nakama, T. / Fukai, S. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Structural basis for anticodon recognition by methionyl-tRNA synthetase. Authors: Nakanishi, K. / Ogiso, Y. / Nakama, T. / Fukai, S. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2csx.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2csx.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 2csx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/2csx ftp://data.pdbj.org/pub/pdb/validation_reports/cs/2csx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24185.381 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 59017.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ (DE3) / References: UniProt: O67298, methionine-tRNA ligase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 % | ||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793, 0.9796, 0.9820 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2004 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→40 Å / % possible obs: 97.8 % / Biso Wilson estimate: 42.2 Å2 | ||||||||||||
Reflection shell | Resolution: 2.7→2.7 Å / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→38.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3260693.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.85 Å2 / ksol: 0.293271 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→38.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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