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Yorodumi- PDB-5zkf: Crystal Structure of N-terminal Domain of Plasmodium vivax p43 in... -
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-Basic information
Entry | Database: PDB / ID: 5zkf | ||||||
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Title | Crystal Structure of N-terminal Domain of Plasmodium vivax p43 in space group P21 | ||||||
Components | Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43 | ||||||
Keywords | LIGASE / GST-like domain / AIMP1 / Plasmodium | ||||||
Function / homology | tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / ligase activity / Glutathione S-transferase, C-terminal domain superfamily / tRNA binding / Nucleic acid-binding, OB-fold / (malaria parasite P. vivax) hypothetical protein / Methionine-tRNA ligase, putative Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | ||||||
Authors | Gupta, S. / Sharma, M. / Harlos, K. / Manickam, Y. / Sharma, A. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein. Authors: Gupta, S. / Chhibber-Goel, J. / Sharma, M. / Parvez, S. / Harlos, K. / Sharma, A. / Yogavel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zkf.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zkf.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zkf ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zkf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21811.281 Da / Num. of mol.: 4 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_120068600, PVP01_1264700, PVT01_120069000 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1G4HHT8, UniProt: A5K3Y7*PLUS #2: 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: 2.08 Å3/Da / Density % sol: 40.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 20 % w/v 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: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.748→45.35 Å / Num. obs: 18633 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 844 / CC1/2: 0.4 / % possible all: 89.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→43.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.3581 / WRfactor Rwork: 0.2692 / FOM work R set: 0.7509 / SU B: 40.205 / SU ML: 0.353 / SU Rfree: 0.1007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: 134.51 Å2 / Biso mean: 58.312 Å2 / Biso min: 29.96 Å2
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Refinement step | Cycle: final / Resolution: 2.75→43.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.748→2.819 Å / Rfactor Rfree error: 0 / 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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