+Open data
-Basic information
Entry | Database: PDB / ID: 3prh | ||||||
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Title | tryptophanyl-tRNA synthetase Val144Pro mutant from B. subtilis | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / TrpRS / protein biosynthesis / translation / class I tRNA synthetase / Rossmann fold / HIGH motif / KMSKS motif / Aminoacyl-tRNA synthetase / ATP-binding / nucleotide-binding | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Antonczak, A.K. / Simova, Z. / Yonemoto, I. / Bochtler, M. / Piasecka, A. / Czapinska, H. / Brancale, A. / Tippmann, E.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Importance of single molecular determinants in the fidelity of expanded genetic codes. Authors: Antonczak, A.K. / Simova, Z. / Yonemoto, I.T. / Bochtler, M. / Piasecka, A. / Czapinska, H. / Brancale, A. / Tippmann, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3prh.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3prh.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 3prh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/3prh ftp://data.pdbj.org/pub/pdb/validation_reports/pr/3prh | HTTPS FTP |
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-Related structure data
Related structure data | 3fio 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: 43893.391 Da / Num. of mol.: 2 / Mutation: V144P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 Gene: 939361, BSU11420, synthetic gene codon optimized for Escherichia coli, trpS Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21656, tryptophan-tRNA ligase |
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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: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05 M MgCl2, 0.05 M HEPES/NaOH pH 7, 25% PEG550, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9805 / Wavelength: 0.9805 Å |
Detector | Type: ADSC / Detector: CCD / Date: Jan 24, 2010 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SINGLE BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9805 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 19307 / Num. obs: 19307 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2763 / Rsym value: 0.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FIO 3fio Resolution: 2.8→29.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.475 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.543 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4123 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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