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Yorodumi- PDB-6hhv: Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-asp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hhv | ||||||||||||
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Title | Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine | ||||||||||||
Components | Aspartate--tRNA(Asp) ligase | ||||||||||||
Keywords | LIGASE / protein-inhibitor complex / tRNA aminoacylation | ||||||||||||
Function / homology | Function and homology information aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Thermus thermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||||||||
Authors | De Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hhv.cif.gz | 442.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hhv.ent.gz | 361.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hhv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6hhv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6hhv_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 6hhv_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhv ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhv | HTTPS FTP |
-Related structure data
Related structure data | 6hdzC 6he1C 6he3C 6hhwC 6hhxC 6hhyC 6hhzC 6hi0C 6rltC 6rluC 6rlvC 6s30C 6sjcC 1l0wS 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: 66181.828 Da / Num. of mol.: 2 / Fragment: aspartyl-tRNA synthetase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: aspS / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS References: UniProt: P36419, UniProt: Q5SKD2*PLUS, aspartate-tRNA ligase #2: Chemical | #3: 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: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were ...Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were grown by mixing an equal volume of the protein solution with 8-12% PEG 4000, 0.1 M Morpheus buffer system 1 (MES/imidazole) pH 7, 100 mM KCl, 20 v/v % glycerol. For soaking a 4 mM solution of compound in DMSO was used. A one third volume of the initial drop size was pipetted carefully onto the crystal containing drop. The sample was then placed back over the reservoir and incubated for approximately 2 hr. Crystals we caught in cryoloops and directly flash frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→67.283 Å / Num. obs: 90892 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L0W Resolution: 2.18→67.283 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.37 Å2 / Biso mean: 65.1497 Å2 / Biso min: 31.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→67.283 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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