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Yorodumi- PDB-3nen: Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nen | ||||||
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Title | Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis | ||||||
Components | Aspartyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / Rossmann fold Ob fold / Aspartic acid / ATP-Mg / tRNA | ||||||
Function / homology | Function and homology information aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / magnesium ion binding / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schmitt, E. / Moras, D. / Moulinier, L. | ||||||
Citation | Journal: Embo J. / Year: 1998 Title: Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation Authors: Schmitt, E. / Moulinier, L. / Fujiwara, S. / Imanaka, T. / Thierry, J.C. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nen.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nen.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nen_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 3nen_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 3nen_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 3nen_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/3nen ftp://data.pdbj.org/pub/pdb/validation_reports/ne/3nen | HTTPS FTP |
-Related structure data
Related structure data | 1b8aC 3nelC 3nemC 1aszS 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
#1: Protein | Mass: 50979.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: aspS, TK0492 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101Tr / References: UniProt: Q52428, aspartate-tRNA ligase #2: 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: 3.32 Å3/Da / Density % sol: 62.99 % |
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Crystal grow | Temperature: 297 K Details: peg and ethylen glycol, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 1996 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.268 Å / Num. obs: 48410 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.099 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ASZ Resolution: 2.4→37.27 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→37.27 Å
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Refine LS restraints |
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