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Yorodumi- PDB-1vbm: Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vbm | ||||||
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Title | Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kobayashi, T. / Sakamoto, K. / Takimura, T. / Kamata, K. / Sekine, R. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. Authors: Kobayashi, T. / Takimura, T. / Sekine, R. / Kelly, V.P. / Vincent, K. / Kamata, K. / Sakamoto, K. / Nishimura, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbm.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbm.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbm ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbm | HTTPS FTP |
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-Related structure data
Related structure data | 1x8xC 1udf 1udj S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35697.352 Da / Num. of mol.: 2 / Fragment: residues 5-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P00951, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.49 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulphate, PEG 400, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9843 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 31, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9843 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 26094 / Num. obs: 23041 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1023 / Rsym value: 0.189 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UDF 1udf Resolution: 2.7→38.54 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2241811.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.7515 Å2 / ksol: 0.345394 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→38.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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