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- PDB-7zog: Crystal structure of Cryptosporidium parvum -Plasmodium falciparu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zog | |||||||||
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Title | Crystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor | |||||||||
![]() | Lysine-tRNA ligase | |||||||||
![]() | LIGASE / tRNA binding | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Dawson, A. / Wyllie, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Toolkit of Approaches To Support Target-Focused Drug Discovery for Plasmodium falciparum Lysyl tRNA Synthetase. Authors: Milne, R. / Wiedemar, N. / Corpas-Lopez, V. / Moynihan, E. / Wall, R.J. / Dawson, A. / Robinson, D.A. / Shepherd, S.M. / Smith, R.J. / Hallyburton, I. / Post, J.M. / Dowers, K. / Torrie, L.S. ...Authors: Milne, R. / Wiedemar, N. / Corpas-Lopez, V. / Moynihan, E. / Wall, R.J. / Dawson, A. / Robinson, D.A. / Shepherd, S.M. / Smith, R.J. / Hallyburton, I. / Post, J.M. / Dowers, K. / Torrie, L.S. / Gilbert, I.H. / Baragana, B. / Patterson, S. / Wyllie, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 439.8 KB | Display | ![]() |
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PDB format | ![]() | 355.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 81.9 KB | Display | |
Data in CIF | ![]() | 122.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hcwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 61464.109 Da / Num. of mol.: 4 / Mutation: P272T, N293V, A309S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Iowa II / Gene: cgd4_2370 / Production host: ![]() ![]() #2: Chemical | ChemComp-LYS / #3: Chemical | ChemComp-JE5 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % / Description: rod |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: Reservoir: 0.1 M tris, pH 7.8, 0.2 M lithium sulfate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→64.9 Å / Num. obs: 226134 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1234 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HCW Resolution: 1.8→64.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.434 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→64.9 Å
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Refine LS restraints |
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