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Yorodumi- PDB-1wle: Crystal Structure of mammalian mitochondrial seryl-tRNA synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wle | ||||||
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Title | Crystal Structure of mammalian mitochondrial seryl-tRNA synthetase complexed with seryl-adenylate | ||||||
Components | Seryl-tRNA synthetase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information : / mitochondrial seryl-tRNA aminoacylation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / tRNA binding / mitochondrial matrix / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Chimnaronk, S. / Jeppesen, M.G. / Suzuki, T. / Nyborg, J. / Watanabe, K. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria Authors: Chimnaronk, S. / Jeppesen, M.G. / Suzuki, T. / Nyborg, J. / Watanabe, K. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase Authors: Yokogawa, T. / Shimada, N. / Takeuchi, N. / Benkowski, L. / Suzuki, T. / Omori, A. / Ueda, T. / Nishikawa, K. / Spremulli, L.L. / Watanabe, K. #2: Journal: J.Biol.Chem. / Year: 2001 Title: Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase Authors: Shimada, N. / Suzuki, T. / Watanabe, K. #3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Crystallization and preliminary X-ray diffraction study of mammalian mitochondrial seryl-tRNA synthetase Authors: Chimnaronk, S. / Jeppesen, M.G. / Shimada, N. / Suzuki, T. / Nyborg, J. / Watanabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wle.cif.gz | 209.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wle.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wle ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wle | HTTPS FTP |
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-Related structure data
Related structure data | 1sryS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer found in the asymmetric unit. |
-Components
#1: Protein | Mass: 56563.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: SerRSmt / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta (Novagen) / References: UniProt: Q9N0F3, serine-tRNA ligase #2: Chemical | #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: 2.8 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 8000, lithium sulfate, MES-NaOH, DTT, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2003 / Details: Bent mirror |
Radiation | Monochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→99 Å / Num. all: 145408 / Num. obs: 145408 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.206 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9594 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SRY Resolution: 1.65→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: THROUGHOUT / Bsol: 63.3399 Å2 / ksol: 0.483133 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5261 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.7 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: SMP.PARAM / Topol file: SMP.TOP |