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Yorodumi- PDB-7zog: Crystal structure of Cryptosporidium parvum -Plasmodium falciparu... -
+Open data
-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 | ||||||
Components | Lysine-tRNA ligaseLysine—tRNA ligase | ||||||
Keywords | LIGASE / tRNA binding | ||||||
Function / homology | Function and homology information lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum Iowa II (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dawson, A. / Wyllie, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zog.cif.gz | 441.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zog.ent.gz | 355.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/7zog ftp://data.pdbj.org/pub/pdb/validation_reports/zo/7zog | HTTPS FTP |
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-Related structure data
Related structure data | 6hcwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0
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.) Cryptosporidium parvum Iowa II (eukaryote) Strain: Iowa II / Gene: cgd4_2370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CR27, lysine-tRNA ligase #2: Chemical | ChemComp-JE5 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-LYS / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.53 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å |
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: 26.844 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.055 / Χ2: 1 / 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: 11209 / CC1/2: 0.84 / Rpim(I) all: 0.616 / Χ2: 1.05 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.19 Å2 / Biso mean: 32.533 Å2 / Biso min: 18.5 Å2
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Refinement step | Cycle: final / Resolution: 1.8→64.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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