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Open data
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Basic information
Entry | Database: PDB / ID: 3s7t | ||||||
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Title | Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic | ||||||
![]() | Putative uncharacterized protein yvmC | ||||||
![]() | LIGASE / Rossmann Fold / tRNA / cyclodipeptide | ||||||
Function / homology | ![]() cyclo(L-leucyl-L-leucyl) synthase / pigment biosynthetic process / aminoacyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonnefond, L. / Ishitani, R. / Nureki, O. | ||||||
![]() | ![]() Title: Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog. Authors: Bonnefond, L. / Arai, T. / Sakaguchi, Y. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 444.4 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30084.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % / Mosaicity: 0.389 ° / Mosaicity esd: 0.004 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 10000 14%, NaCl 100mM, 20% glycerol, pH 8.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 15530 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.148 / Χ2: 3.552 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.351 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.69 Å2 / Biso mean: 25.8158 Å2 / Biso min: 8.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.808→38.871 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: 11
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