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Yorodumi- PDB-3oqj: Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oqj | ||||||
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Title | Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CAPSO | ||||||
Components | Putative uncharacterized protein yvmC | ||||||
Keywords | LIGASE / tRNA / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information cyclo(L-leucyl-L-leucyl) synthase / pigment biosynthetic process / aminoacyltransferase activity Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.399 Å | ||||||
Authors | Bonnefond, L. / Arai, T. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oqj.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oqj.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 3oqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oqj_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 3oqj_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 3oqj_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3oqj_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oqj ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oqj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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.: 2 Source method: isolated from a genetically manipulated source Details: NdeI/XhoI restriction sites / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: ATCC 14580 / Gene: BL00817, BLi03566, yvmC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q65EX3 #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: 2.69 Å3/Da / Density % sol: 54.23 % / Mosaicity: 0.329 ° |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5 % / Av σ(I) over netI: 21.73 / Number: 125460 / Rmerge(I) obs: 0.077 / Χ2: 1.09 / D res high: 2.399 Å / D res low: 50 Å / Num. obs: 24915 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.399→50 Å / Num. obs: 24915 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Χ2: 1.091 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.399→38.63 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8474 / SU ML: 0.32 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.409 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.38 Å2 / Biso mean: 32.6675 Å2 / Biso min: 13.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.399→38.63 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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