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Yorodumi- PDB-3p0h: Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p0h | ||||||
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Title | Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / tRNA ligase / aaRS / TyrRS / pseudodimer / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ciliary plasm / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / molecular replacement / SAD / Resolution: 3 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Double-Length Tyrosyl-tRNA Synthetase from the Eukaryote Leishmania major Forms an Intrinsically Asymmetric Pseudo-Dimer. Authors: Larson, E.T. / Kim, J.E. / Castaneda, L.J. / Napuli, A.J. / Zhang, Z. / Fan, E. / Zucker, F.H. / Verlinde, C.L. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p0h.cif.gz | 500.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p0h.ent.gz | 415.5 KB | Display | PDB format |
PDBx/mmJSON format | 3p0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p0h_validation.pdf.gz | 951.5 KB | Display | wwPDB validaton report |
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Full document | 3p0h_full_validation.pdf.gz | 967.7 KB | Display | |
Data in XML | 3p0h_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 3p0h_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/3p0h ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p0h | HTTPS FTP |
-Related structure data
Related structure data | 3p0iC 3p0jC 2cyaS 2cycS 2j5bS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 77057.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF14.1370 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QFJ7, tyrosine-tRNA ligase #2: Chemical | |
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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: 3.75 Å3/Da / Density % sol: 67.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v ...Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v acetone); cryoprotected by addition of 30% PEG 3350, 10% MSGPP buffer, 10% ethylene glycol, and 0.1 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→47.11 Å / Num. obs: 46076 / % possible obs: 99.95 % / Redundancy: 13.81 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 14.0489 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing |
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Phasing dm | FOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.69 / Reflection: 46076 / Reflection acentric: 43572 / Reflection centric: 2504 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, SAD Starting model: Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion. Resolution: 3→47.11 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 39.529 / SU ML: 0.324 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 266.36 Å2 / Biso mean: 80.8342 Å2 / Biso min: 29.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→47.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 7569 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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