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Yorodumi- PDB-2ip1: Crystal Structure Analysis of S. cerevisiae Tryptophanyl tRNA Syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ip1 | ||||||
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Title | Crystal Structure Analysis of S. cerevisiae Tryptophanyl tRNA Synthetase | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / rossmann fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Malkowski, M.G. / Center for High-Throughput Structural Biology (CHTSB) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing. Authors: Malkowski, M.G. / Quartley, E. / Friedman, A.E. / Babulski, J. / Kon, Y. / Wolfley, J. / Said, M. / Luft, J.R. / Phizicky, E.M. / DeTitta, G.T. / Grayhack, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ip1.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ip1.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ip1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/2ip1 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2ip1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 49419.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: WRS1 / Plasmid: BG2483 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12109, tryptophan-tRNA ligase | ||
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#2: Chemical | ChemComp-PG4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 7 Details: 80% PEG 400, 100 mM NH4Br, 100mM MOPS, pH 7.0, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97935, 0.97952, 0.96109 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2006 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→40 Å / Num. all: 45665 / Num. obs: 45655 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9 | ||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4942 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→39.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.921 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.837 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→39.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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