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Yorodumi- PDB-2j5b: Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j5b | ||||||
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Title | Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol | ||||||
Components | TYROSYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / PROTEIN BIOSYNTHESIS / ATP-BINDING | ||||||
Function / homology | Function and homology information L-tyrosine binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ACANTHAMOEBA POLYPHAGA MIMIVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Abergel, C. / Rudinger-thirion, J. / Giege, R. / Claverie, J.M. | ||||||
Citation | Journal: J.Virol. / Year: 2007 Title: Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus Tyrrs and Metrs. Authors: Abergel, C. / Rudinger-Thirion, J. / Giege, R. / Claverie, J.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Mimivirus Tyrrs: Preliminary Structural and Functional Characterization of the First Amino- Acyl tRNA Synthetase Found in a Virus. Authors: Abergel, C. / Chenivesse, S. / Byrne, D. / Suhre, K. / Arondel, V. / Claverie, J.-M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j5b.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j5b.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j5b ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j5b | 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: (Code: given Matrix: (-0.10962, -0.99355, -0.02886), Vector: |
-Components
#1: Protein | Mass: 39895.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACANTHAMOEBA POLYPHAGA MIMIVIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q5UPJ7, tyrosine-tRNA ligase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | N TERMINAL EXTENSION DUE TO GATEWAY CLONING | |
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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: 3.17 Å3/Da / Density % sol: 61.18 % Description: STRUCTURE WAS SOLVED USING TYRRS WITH SELENO SUBSTITUTED METHIONINE AND INCOMPLETE MAD DATASET AT 3.5 AMGSTROM RESOLUTION. THE UNREFINED CONSTRUCTION WAS USED AS MODEL FOR MOLECULAR ...Description: STRUCTURE WAS SOLVED USING TYRRS WITH SELENO SUBSTITUTED METHIONINE AND INCOMPLETE MAD DATASET AT 3.5 AMGSTROM RESOLUTION. THE UNREFINED CONSTRUCTION WAS USED AS MODEL FOR MOLECULAR REPLACEMENT WITH THE NATIVE DATASET |
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Crystal grow | pH: 5.5 Details: RESERVOIR: 0.1 M SODIUM CITRATE BUFFER PH 5.5, PEG 4000 8% (W/V), 15% MPD (V/V), 0.1M KCL, 1MM MGCL2 DROPLET: 2 MICROL TYRRS 14 MG/ML IN 20 MM TRIS PH 7.4, 1MM TYROSINOL, 1MM ATP 0.5 MICROL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97925 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006 / Details: MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→87 Å / Num. obs: 52537 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LOW RESOLUTION MAD STRUCTURE Resolution: 2.2→29.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2137340.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAIN A WAS NOT MODELED. DISORDERED REGION 142 TO 158 CHAIN B WAS NOT MODELED. DISORDERED REGION 223 TO 226 CHAIN B WAS MODELED USING RESIDUAL DENSITY AND STEREOCHEMISTRY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.7184 Å2 / ksol: 0.32568 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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