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Yorodumi- PDB-1asy: CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1asy | ||||||
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Title | CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF YEAST ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH TRNA ASP | ||||||
Components |
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Keywords | COMPLEX (AMINOACYL-TRNA SYNTHASE/TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) complex | ||||||
Function / homology | Function and homology information aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Ruff, M. / Cavarelli, J. / Rees, B. / Krishnaswamy, S. / Thierry, J.C. / Moras, D. | ||||||
Citation | Journal: Science / Year: 1991 Title: Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Authors: Ruff, M. / Krishnaswamy, S. / Boeglin, M. / Poterszman, A. / Mitschler, A. / Podjarny, A. / Rees, B. / Thierry, J.C. / Moras, D. #1: Journal: Embo J. / Year: 1994 Title: The Active Site of Yeast Aspartyl-tRNA Synthetase: Structural and Functional Aspects of the Aminoacylation Reaction Authors: Cavarelli, J. / Eriani, G. / Rees, B. / Ruff, M. / Boeglin, M. / Mitschler, A. / Martin, F. / Gangloff, J. / Thierry, J.C. / Moras, D. #2: Journal: Biochimie / Year: 1993 Title: Yeast Aspartyl-tRNA Synthetase: A Structural View of the Aminoacylation Reaction Authors: Cavarelli, J. / Rees, B. / Thierry, J.C. / Moras, D. #3: Journal: Nature / Year: 1993 Title: Yeast tRNA Asp Recognition by its Cognate Class II Aminoacyl-tRNA Synthetase Authors: Cavarelli, J. / Rees, B. / Ruff, M. / Thierry, J.C. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1asy.cif.gz | 289.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1asy.ent.gz | 227.3 KB | Display | PDB format |
PDBx/mmJSON format | 1asy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/1asy ftp://data.pdbj.org/pub/pdb/validation_reports/as/1asy | 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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Atom site foot note | 1: CIS PROLINE - PRO A 557 / 2: CIS PROLINE - PRO B 557 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99055, -0.05698, -0.12477), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 68 .. R 676 B 68 .. S 676 1.04 | |
-Components
#1: RNA chain | Mass: 24181.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: aspartate-tRNA ligase #2: Protein | Mass: 56026.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P04802 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1988 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 67061 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 |
-Processing
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Refinement | Resolution: 2.9→7 Å / σ(F): 3 Details: TRNA RIBOSES 607, 609, 617, 618, 619, 637, 648, 658, 660, 676, FROM EACH CHAIN, HAVE BEEN CONSTRAINED TO 2' ENDO PUCKER. ALL OTHER TRNA RIBOSES ARE 3' ENDO PUCKER.
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Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→7 Å
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Refine LS restraints |
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