+Open data
-Basic information
Entry | Database: PDB / ID: 8hyr | |||||||||
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Title | Crystal structure of human KARS apo | |||||||||
Components | Lysine--tRNA ligase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Lysyl-tRNA synthetase / KARS | |||||||||
Function / homology | Function and homology information basophil activation involved in immune response / ATP:ADP adenylyltransferase activity / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex ...basophil activation involved in immune response / ATP:ADP adenylyltransferase activity / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / Resolution: 2.55 Å | |||||||||
Authors | Zhang, X. / Wang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of human KARS apo Authors: Zhang, X. / Wang, Y. / Ouyang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hyr.cif.gz | 717.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hyr.ent.gz | 502.1 KB | Display | PDB format |
PDBx/mmJSON format | 8hyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hyr_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 8hyr_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 8hyr_validation.xml.gz | 37 KB | Display | |
Data in CIF | 8hyr_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/8hyr ftp://data.pdbj.org/pub/pdb/validation_reports/hy/8hyr | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), (-0.00654785426751, 0.999920918381, -0.0107369729668), (-0.000959491357428, -0.0107434805843, -0.999941826809) ...NCS oper: (Code: given Matrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), Vector: |
-Components
#1: Protein | Mass: 60197.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KARS1, KARS, KIAA0070 / Production host: Escherichia phage EcSzw-2 (virus) References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-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: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer system 1, pH 6.5, 30% Morpheus Precipitant Mix 2 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 42172 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.064 / Rrim(I) all: 0.165 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.93 / Num. unique obs: 4151 / CC1/2: 0.865 / Rpim(I) all: 0.383 / Rrim(I) all: 0.961 / % possible all: 99.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.24 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9554 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→46.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.515430016446 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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