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- PDB-3oms: Putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oms | ||||||
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Title | Putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus. | ||||||
![]() | PhnB protein | ||||||
![]() | TRANSFERASE / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / methyltransferase / glyoxalase family | ||||||
Function / homology | ![]() Signal recognition particle alu RNA binding heterodimer, srp9/1 - #100 / Predicted 3-demethylubiquinone-9 3-methyltransferase, bacterial / Predicted 3-demethylubiquinone-9 3-methyltransferase / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / PhnB-like / 3-demethylubiquinone-9 3-methyltransferase / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: X-ray crystal structure of putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus. Authors: Osipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.9 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.6 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15877.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 40% PEG-300, 0.1 M phoshate citrate buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 11, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→36.7 Å / Num. all: 14643 / Num. obs: 14643 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.138 / Χ2: 3.39 / Net I/σ(I): 7.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 59.23 Å2 / Biso mean: 37.193 Å2 / Biso min: 10.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.952 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.6391 Å / Origin y: 11.5424 Å / Origin z: 36.6645 Å
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