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Yorodumi- PDB-1ulh: A short peptide insertion crucial for angiostatic activity of hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ulh | ||||||
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Title | A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacylation / angiostatic cytokine / apoptosis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 Å | ||||||
Authors | Kise, Y. / Sengoku, T. / Ishii, R. / Yokoyama, S. / Park, S.G. / Lee, S.W. / Kim, S. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase Authors: Kise, Y. / Lee, S.W. / Park, S.G. / Fukai, S. / Sengoku, T. / Ishii, R. / Yokoyama, S. / Kim, 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 | 1ulh.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ulh.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ulh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/1ulh ftp://data.pdbj.org/pub/pdb/validation_reports/ul/1ulh | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 44791.934 Da / Num. of mol.: 2 / Fragment: residues 35-424 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: trps / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase #2: 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: 2.71 Å3/Da / Density % sol: 54.32 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 10000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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: 0.9799 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2002 / Details: mirror |
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. all: 277220 / Num. obs: 106623 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.056 |
Reflection shell | Resolution: 2.31→50 Å / Rsym value: 0.215 / % possible all: 76.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 76.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.31→42.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1552705 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.6502 Å2 / ksol: 0.333583 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→42.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.45 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.229 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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