+Open data
-Basic information
Entry | Database: PDB / ID: 1b8a | ||||||
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Title | ASPARTYL-TRNA SYNTHETASE | ||||||
Components | PROTEIN (ASPARTYL-TRNA SYNTHETASE) | ||||||
Keywords | LIGASE / SYNTHETASE / TRNA LIGASE | ||||||
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: 1.9 Å | ||||||
Authors | Schmitt, E. / Moulinier, L. / Thierry, J.-C. / Moras, D. | ||||||
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 | 1b8a.cif.gz | 221.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8a.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8a ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8a | HTTPS FTP |
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-Related structure data
Related structure data | 3nelC 3nemC 3nenC 1aszS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0651, 0.9967, -0.049), Vector: |
-Components
#1: Protein | Mass: 50980.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Cellular location: CYTOPLASM / Gene: ASPS / Plasmid: PUC18F / Production host: Escherichia coli (E. coli) / References: UniProt: Q52428, aspartate-tRNA ligase #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: 3.33 Å3/Da / Density % sol: 63.09 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 3916674 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 8.2 Å2 / Rsym value: 5 |
Reflection | *PLUS Num. obs: 105560 / Num. measured all: 3916674 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Rmerge(I) obs: 0.269 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ASZ Resolution: 1.9→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2674497.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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