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Yorodumi- PDB-5gro: Crystal structure of the N-terminal anticodon-binding domain of n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gro | |||||||||
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Title | Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori | |||||||||
Components | Aspartate--tRNA(Asp/Asn) ligase | |||||||||
Keywords | LIGASE / non-discriminating aspartyl-tRNA synthetase / anticodon-binding domain / Helicobacter pylori | |||||||||
Function / homology | Function and homology information aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Helicobacter pylori 26695 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Songsiriritthigul, C. / Fuengfuloy, P. / Chen, C.-J. / Suebka, S. / Chuawong, P. | |||||||||
Funding support | Thailand, 2items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori Authors: Songsiriritthigul, C. / Suebka, S. / Chen, C.-J. / Fuengfuloy, P. / Chuawong, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gro.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gro.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gro_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
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Full document | 5gro_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 5gro_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5gro_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/5gro ftp://data.pdbj.org/pub/pdb/validation_reports/gr/5gro | HTTPS FTP |
-Related structure data
Related structure data | 1c0aS 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: 12896.983 Da / Num. of mol.: 2 Fragment: N-TERMINAL ANTICODON BINDING DOMAIN, UNP residues 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: aspS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56459, aspartate-tRNAAsn ligase #2: Chemical | #3: Chemical | ChemComp-BUA / | #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 7% (w/v) PEG 4000, 0.1 M ammonium sulfate, 0.1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 19187 / % possible obs: 98.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C0A Resolution: 2→27.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.406 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.132 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.04 Å2 / Biso mean: 33.408 Å2 / Biso min: 20.12 Å2
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Refinement step | Cycle: final / Resolution: 2→27.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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