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Yorodumi- PDB-8p1z: Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p1z | ||||||
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Title | Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT) | ||||||
Components | Serine--tRNA ligase, cytoplasmic | ||||||
Keywords | CYTOSOLIC PROTEIN / synthetase / class II / cytoplasmic | ||||||
Function / homology | Function and homology information seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / plastid / cytoplasmic translation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kekez, I. / Soic, R. / Rokov-Plavec, J. / Matkovic-Calogovic, D. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: To Be Published Title: Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT) Authors: Kekez, I. / Soic, R. / Rokov-Plavec, J. / Matkovic-Calogovic, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p1z.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p1z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1z ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1z | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52143.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Parts of the sequence that are not visible from the electron density map and are missing in pdb file. Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g27470, F21A20_180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39230, serine-tRNA ligase |
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#2: 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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride, PEG 4000, TRIS pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.167 Å / Num. obs: 20826 / % possible obs: 97.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.3→2.39 Å / Rmerge(I) obs: 0.816 / Num. unique obs: 2088 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.158 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.207 / SU B: 16.306 / SU ML: 0.341 / Average fsc free: 0.7249 / Average fsc work: 0.7458 / Cross valid method: FREE R-VALUE / ESU R: 0.382 / ESU R Free: 0.279 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.999 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.158 Å
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Refine LS restraints |
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LS refinement shell |
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