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Yorodumi- PDB-7lu4: Crystal structure of bacterial glycyl tRNA synthetase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lu4 | |||||||||
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Title | Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine | |||||||||
Components | Multifunctional fusion protein | |||||||||
Keywords | LIGASE / RNA binding protein / tRNA synthetase | |||||||||
Function / homology | Function and homology information glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermanaerothrix daxensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Torres-Larios, A. | |||||||||
Funding support | Mexico, 2items
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Citation | Journal: To Be Published Title: Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine Authors: Torres-Larios, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lu4.cif.gz | 377.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lu4.ent.gz | 299.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lu4_validation.pdf.gz | 744.4 KB | Display | wwPDB validaton report |
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Full document | 7lu4_full_validation.pdf.gz | 759.9 KB | Display | |
Data in XML | 7lu4_validation.xml.gz | 61 KB | Display | |
Data in CIF | 7lu4_validation.cif.gz | 83.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/7lu4 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7lu4 | HTTPS FTP |
-Related structure data
Related structure data | 5f5wS 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
#1: Protein | Mass: 113698.430 Da / Num. of mol.: 2 / Mutation: All Cys to Ser Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermanaerothrix daxensis (bacteria) / Gene: glyS, glyQ, SE15_09895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0P6Y0P9, glycine-tRNA ligase #2: Chemical | ChemComp-GLY / | Has ligand of interest | Y | |
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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: 4.34 Å3/Da / Density % sol: 71.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 550 mM Magnesium formate, 100 mM sodium acetate, 1% sodium dextran sulfate 4000, 100 mM glycine pH 8.5, 3% sacarose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.62 Å / Num. obs: 132960 / % possible obs: 99.2 % / Redundancy: 17.1 % / Biso Wilson estimate: 72.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.045 / Rrim(I) all: 0.134 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6548 / CC1/2: 0.452 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5f5w Resolution: 2.5→35.74 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→35.74 Å
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Refine LS restraints |
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LS refinement shell |
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