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- PDB-3oqi: Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oqi | ||||||
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Title | Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CHES | ||||||
![]() | (Putative uncharacterized protein yvmC) x 2 | ||||||
![]() | LIGASE / tRNA / ROSSMANN FOLD | ||||||
Function / homology | ![]() cyclo(L-leucyl-L-leucyl) synthase / pigment biosynthetic process / aminoacyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bonnefond, L. / Arai, T. / Suzuki, T. / 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 | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 87.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
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Full document | ![]() | 466.5 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 34 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: 29662.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NdeI/XhoI restriction sites / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 29694.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NdeI/XhoI restriction sites / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-NHE / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % / Mosaicity: 0.282 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 20% PEG 8000, pH 9.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.5 % / Av σ(I) over netI: 29.72 / Number: 529353 / Rmerge(I) obs: 0.085 / Χ2: 1.18 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 70129 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 70129 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.085 / Χ2: 1.181 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.142 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.68 Å2 / Biso mean: 17.7777 Å2 / Biso min: 5.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.701→32.354 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: 10
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