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Yorodumi- PDB-3kfl: Leishmania major methionyl-tRNA synthetase in complex with methio... -
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-Basic information
Entry | Database: PDB / ID: 3kfl | ||||||
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Title | Leishmania major methionyl-tRNA synthetase in complex with methionyladenylate and pyrophosphate | ||||||
Components | Methionyl-tRNA synthetase | ||||||
Keywords | LIGASE / Leishmania / parasite / aminoacyl-tRNA synthetase / tRNA ligase / aaRS / MetRS / methionine / translation / ATP-binding / nucleotide-binding / Structural Genomics / MSGPP / Medical Structural Genomics of Pathogenic Protozoa | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | Journal: Biochimie / Year: 2011 Title: Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. Authors: Larson, E.T. / Kim, J.E. / Zucker, F.H. / Kelley, A. / Mueller, N. / Napuli, A.J. / Verlinde, C.L. / Fan, E. / Buckner, F.S. / Van Voorhis, W.C. / Merritt, E.A. / 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 | 3kfl.cif.gz | 237.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kfl.ent.gz | 188.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kfl_validation.pdf.gz | 735.6 KB | Display | wwPDB validaton report |
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Full document | 3kfl_full_validation.pdf.gz | 736.2 KB | Display | |
Data in XML | 3kfl_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 3kfl_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfl ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfl | HTTPS FTP |
-Related structure data
Related structure data | 2csxS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63984.793 Da / Num. of mol.: 1 / Fragment: UNP residues 206-747 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF21.0810, MetRS / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QCD2, methionine-tRNA ligase |
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-Non-polymers , 7 types, 232 molecules
#2: Chemical | ChemComp-ME8 / [[( | ||||
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#3: Chemical | ChemComp-POP / | ||||
#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | ChemComp-ZN / | ||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-FMT / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K- ...Details: 2 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K-formate, 26% PEG 3350 and additives of 10 mM L-Met and 1 mM TCEP]; crystal cryoprotected by quick soak in mother liquor supplemented with 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97923 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 23, 2009 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 42546 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 5.3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2csx Resolution: 2→37.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.108 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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 mean: 38.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.16 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: 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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