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Yorodumi- PDB-3qo5: Crystal Structure of the seryl-tRNA synthetase from Candida albicans -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qo5 | ||||||
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Title | Crystal Structure of the seryl-tRNA synthetase from Candida albicans | ||||||
Components | Seryl-tRNA synthetase, cytoplasmic | ||||||
Keywords | LIGASE / genetic code ambiguity / tRNA / class-II aminoacyl-tRNA synthetase family / Type-1 seryl-tRNA synthetase subfamily / tRNA aminoacylation / serine | ||||||
Function / homology | Function and homology information seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / cytoplasmic translation / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rocha, R. / Santos, M.A. / Pereira, P.J.B. / Macedo-Ribeiro, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen. Authors: Rocha, R. / Pereira, P.J. / Santos, M.A. / Macedo-Ribeiro, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Purification, crystallization and preliminary X-ray diffraction analysis of the seryl-tRNA synthetase from Candida albicans. Authors: Rocha, R. / Barbosa Pereira, P.J. / Santos, M.A. / Macedo-Ribeiro, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qo5.cif.gz | 191.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qo5.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qo5 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qo5 | HTTPS FTP |
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-Related structure data
Related structure data | 3qneC 3qo7C 3qo8C 2dq0S C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55708.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: SES1, CaO19.7901 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HGT6, serine-tRNA ligase |
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#2: Water | ChemComp-HOH / |
Sequence details | S197L IS A MINOR ISOFORM (CUG CODON TRANSLATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 3.2-3.4 M ammonium sulfate, 0-2% v/v glycerol, 100 mM MES/sodium, pH 5.6-5.8, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80.1 Å / Num. obs: 31871 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.44 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DQ0 Resolution: 2.3→69.103 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 21.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.961 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→69.103 Å
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Refine LS restraints |
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LS refinement shell |
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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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