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Yorodumi- PDB-6chd: Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6chd | ||||||
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Title | Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine | ||||||
Components | Lysine--tRNA ligase | ||||||
Keywords | LIGASE / TRANSFERASE / ATP binding / aminoacylation / amino acid binding / ATP adenylyltransferase activity / tRNA binding / Structure-guided Drug Discovery Consortium | ||||||
Function / homology | Function and homology information basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation ...basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / mitochondrial matrix / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Dranow, D.M. / Abendroth, J. / Lorimer, D.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine Authors: Dranow, D.M. / Abendroth, J. / Baragana, B. / Walpole, C. / Lorimer, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6chd.cif.gz | 421.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6chd.ent.gz | 342.2 KB | Display | PDB format |
PDBx/mmJSON format | 6chd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6chd_validation.pdf.gz | 927.4 KB | Display | wwPDB validaton report |
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Full document | 6chd_full_validation.pdf.gz | 934.6 KB | Display | |
Data in XML | 6chd_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 6chd_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6chd ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6chd | HTTPS FTP |
-Related structure data
Related structure data | 3bjuS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 68143.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-tRNA ligase |
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-Non-polymers , 5 types, 261 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Human KRS at 35.6 mg/ml, incubated with 5 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with Top96(c3): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-Tris:HCl, pH = 5.5: cryoprotected ...Details: Human KRS at 35.6 mg/ml, incubated with 5 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with Top96(c3): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-Tris:HCl, pH = 5.5: cryoprotected with 20% ethylene glycol. Tray: 297612c3, puck: KYY0-11 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→49.056 Å / Num. obs: 47408 / % possible obs: 100 % / Redundancy: 8.677 % / Biso Wilson estimate: 45.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.093 / Χ2: 1.012 / Net I/σ(I): 16.45 / Num. measured all: 411370 / Scaling rejects: 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3bju Resolution: 2.5→49.056 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.63 Å2 / Biso mean: 52.8766 Å2 / Biso min: 4.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→49.056 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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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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