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Yorodumi- PDB-1i6l: 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i6l | ||||||
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Title | 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP | ||||||
Components | TRYPTOPHANYL- ... | ||||||
Keywords | LIGASE / CLASS I TRNA SYNTHETASE / AARS / INDUCED FIT / TRPRS | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å | ||||||
Authors | Retailleau, P. / Carter, C.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP. Authors: Retailleau, P. / Yin, Y. / Hu, M. / Roach, J. / Bricogne, G. / Vonrhein, C. / Roversi, P. / Blanc, E. / Sweet, R.M. / Carter, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6l.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6l.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i6l_validation.pdf.gz | 781.1 KB | Display | wwPDB validaton report |
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Full document | 1i6l_full_validation.pdf.gz | 792.1 KB | Display | |
Data in XML | 1i6l_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 1i6l_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6l ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-TRYPTOPHANYL- ... , 1 types, 1 molecules A
#1: Protein | Mass: 37694.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P00953, tryptophan-tRNA ligase |
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-Non-polymers , 5 types, 366 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NH4 / | #4: Chemical | ChemComp-TYM / | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.8 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: microdialysis / pH: 7.6 Details: POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM SULFATE, pH 7.60, MICRODIALYSIS, temperature 310K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | |||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 0.979 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Apr 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 51522 / % possible obs: 95.7 % / Redundancy: 10.3 % / Rsym value: 0.078 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.72→1.8 Å / Rsym value: 0.571 / % possible all: 68.8 |
Reflection | *PLUS Redundancy: 5.15 % / Num. measured all: 1045314 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 68.8 % / Rmerge(I) obs: 0.571 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.72→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.72→20 Å
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Refine LS restraints |
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Software | *PLUS Name: BUSTER/TNT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 31909 / % reflection Rfree: 10 % / Rfactor all: 0.209 / Rfactor obs: 0.2 / σ(I): 3 | |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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