+Open data
-Basic information
Entry | Database: PDB / ID: 4j75 | ||||||
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Title | Crystal Structure of a parasite tRNA synthetase, product-bound | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / aaRS / TrpRS / parasite / protein-substrate complex / Rossmann fold / translation / nucleotide binding | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Koh, C.Y. / Kim, J.E. / Verlinde, C.L.M.J. / Hol, W.G.J. | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2013 Title: Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design. Authors: Koh, C.Y. / Kim, J.E. / Napoli, A.J. / Verlinde, C.L. / Fan, E. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j75.cif.gz | 318.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j75.ent.gz | 259.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j75 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j75 | HTTPS FTP |
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-Related structure data
Related structure data | 4j76SC S: Starting model for refinement C: citing same article (ref.) |
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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: 47216.734 Da / Num. of mol.: 2 / Fragment: UNP residues 229-632 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF13_0205 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDW3, tryptophan-tRNA ligase #2: Chemical | #3: Chemical | #4: 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: 3.02 Å3/Da / Density % sol: 59.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 15, 2010 |
Radiation | Monochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.64 Å / Num. obs: 45354 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 2.2 / Num. measured all: 32129 / Num. unique all: 4348 / % possible all: 98.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4J76 Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.471 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 max: 158.41 Å2 / Biso mean: 43.9496 Å2 / Biso min: 13.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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