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Yorodumi- PDB-4ex5: Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ex5 | ||||||
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Title | Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to lysine | ||||||
Components | Lysine--tRNA ligase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminoacyl-tRNA synthetase / lysine tRNA ligase / protein synthesis / ATP-depenedent / tRNAlys / class IIb tRNA synthetase | ||||||
Function / homology | Function and homology information lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ex5.cif.gz | 391.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ex5.ent.gz | 317.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ex5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/4ex5 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4ex5 | HTTPS FTP |
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-Related structure data
Related structure data | 3sp1C 3tzeC 4e51C 4g6zC 4griC 1bbuS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 15 - 601 / Label seq-ID: 36
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-Components
#1: Protein | Mass: 59590.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1883, lysS / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SXD6, lysine-tRNA ligase #2: Chemical | #3: 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: 3.73 Å3/Da / Density % sol: 66.98 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, ...Details: ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, crystal tracking ID 232983h5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 19, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 68404 / Num. obs: 67117 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 39.185 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.87 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1bbu Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2906 / WRfactor Rwork: 0.2532 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.739 / SU B: 10.223 / SU ML: 0.125 / SU R Cruickshank DPI: 0.3455 / SU Rfree: 0.2829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.17 Å2 / Biso mean: 32.9777 Å2 / Biso min: 9.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 17714 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.09 / Type: LOCAL / Weight: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / 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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