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Yorodumi- PDB-5xio: Crystal Structure of Cryptosporidium parvum Prolyl-tRNA Synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xio | ||||||
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Title | Crystal Structure of Cryptosporidium parvum Prolyl-tRNA Synthetase (CpPRS) in complex with Halofuginone | ||||||
Components | Proline-tRNA synthetase class II aaRS (Ybak RNA binding domain plus tRNA synthetase) | ||||||
Keywords | LIGASE / Protein Translation / PRS / Synthetase / Inhibitor / Infectious Disease | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å | ||||||
Authors | Jain, V. / Manickam, Y. / Sharma, A. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis Authors: Jain, V. / Yogavel, M. / Kikuchi, H. / Oshima, Y. / Hariguchi, N. / Matsumoto, M. / Goel, P. / Touquet, B. / Jumani, R.S. / Tacchini-Cottier, F. / Harlos, K. / Huston, C.D. / Hakimi, M.A. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xio.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xio.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xio_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5xio_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5xio_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 5xio_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/5xio ftp://data.pdbj.org/pub/pdb/validation_reports/xi/5xio | HTTPS FTP |
-Related structure data
Related structure data | 5xifC 5xigC 5xihC 5xiiC 5xijC 5xikC 5xilC 5xipC 5xiqC 4twaS C: citing same article (ref.) 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
#1: Protein | Mass: 57638.203 Da / Num. of mol.: 2 / Fragment: UNP residues 225-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd6_4400 / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q5CWN3 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20%(w/v) PEG 3,350 and 0.2M Ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→29.31 Å / Num. obs: 48148 / % possible obs: 99.3 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.46→2.52 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3254 / % possible all: 92 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWA Resolution: 2.46→29.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.374 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 41.513 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→29.31 Å
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