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Yorodumi- PDB-4jfa: Crystal Structure of Plasmodium falciparum Tryptophanyl-tRNA synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jfa | ||||||
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Title | Crystal Structure of Plasmodium falciparum Tryptophanyl-tRNA synthetase | ||||||
Components | Tryptophan--tRNA ligase | ||||||
Keywords | LIGASE / WRS / TrpRS / Plasmodium | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Khan, S. / Garg, A. / Manickam, Y. / Sharma, A. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: An appended domain results in an unusual architecture for malaria parasite tryptophanyl-tRNA synthetase Authors: Khan, S. / Garg, A. / Sharma, A. / Camacho, N. / Picchioni, D. / Saint-Leger, A. / Ribas de Pouplana, L. / Yogavel, M. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jfa.cif.gz | 294 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jfa.ent.gz | 244.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jfa_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
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Full document | 4jfa_full_validation.pdf.gz | 511.8 KB | Display | |
Data in XML | 4jfa_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 4jfa_validation.cif.gz | 72.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/4jfa ftp://data.pdbj.org/pub/pdb/validation_reports/jf/4jfa | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48827.480 Da / Num. of mol.: 4 / Fragment: UNP residues 228-632 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF13_0205 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8IDW3, tryptophan-tRNA ligase #2: Chemical | ChemComp-TRP / #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: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.09M NPS, 0.1M Bicin pH 8.5, 12.5% MPD, 12.4 PEG 1000, 12.5% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2011 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 66294 / Num. obs: 62582 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.11 Å2 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.94 / Num. unique all: 3006 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.83 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8411 / SU ML: 0.21 / σ(F): 1.38 / Phase error: 23.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.27 Å2 / Biso mean: 54.4151 Å2 / Biso min: 10.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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