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- PDB-6hcw: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hcw | ||||||
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Title | Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand | ||||||
![]() | Lysine--tRNA ligase | ||||||
![]() | TRANSFERASE / ADENYLYLTRANSFERASE ACTIVITY / TRNA BINDING / LIGASE | ||||||
Function / homology | ![]() ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robinson, D.A. / Baragana, B. / Norcross, N. / Forte, B. / Walpole, C. / Gilbert, I.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis. Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / ...Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / Anderson, M. / Brooks, C.F. / Cooper, C.A. / Damerow, S. / Delves, M. / Dowers, K. / Duffy, J. / Edwards, T.E. / Hallyburton, I. / Horst, B.G. / Hulverson, M.A. / Ferguson, L. / Jimenez-Diaz, M.B. / Jumani, R.S. / Lorimer, D.D. / Love, M.S. / Maher, S. / Matthews, H. / McNamara, C.W. / Miller, P. / O'Neill, S. / Ojo, K.K. / Osuna-Cabello, M. / Pinto, E. / Post, J. / Riley, J. / Rottmann, M. / Sanz, L.M. / Scullion, P. / Sharma, A. / Shepherd, S.M. / Shishikura, Y. / Simeons, F.R.C. / Stebbins, E.E. / Stojanovski, L. / Straschil, U. / Tamaki, F.K. / Tamjar, J. / Torrie, L.S. / Vantaux, A. / Witkowski, B. / Wittlin, S. / Yogavel, M. / Zuccotto, F. / Angulo-Barturen, I. / Sinden, R. / Baum, J. / Gamo, F.J. / Maser, P. / Kyle, D.E. / Winzeler, E.A. / Myler, P.J. / Wyatt, P.G. / Floyd, D. / Matthews, D. / Sharma, A. / Striepen, B. / Huston, C.D. / Gray, D.W. / Fairlamb, A.H. / Pisliakov, A.V. / Walpole, C. / Read, K.D. / Van Voorhis, W.C. / Gilbert, I.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235 KB | Display | ![]() |
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PDB format | ![]() | 183.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.9 KB | Display | ![]() |
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Full document | ![]() | 1017.7 KB | Display | |
Data in XML | ![]() | 44.7 KB | Display | |
Data in CIF | ![]() | 69.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5elnSC ![]() 5eloC ![]() 6agtC ![]() 6hcuC ![]() 6hcvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61459.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cgd4_2370 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % / Description: cuboid |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris HCl pH 8.5 PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→73 Å / Num. obs: 205432 / % possible obs: 97.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.46→1.5 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.56 / % possible all: 80.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ELN Resolution: 1.46→72.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.397 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.49 Å2 / Biso mean: 15.952 Å2 / Biso min: 5.66 Å2
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Refinement step | Cycle: final / Resolution: 1.46→72.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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