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Yorodumi- PDB-2b81: Crystal Structure of the Luciferase-like Monooxygenase from Bacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b81 | ||||||
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Title | Crystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus | ||||||
Components | Luciferase-like monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Kim, Y. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus Authors: Kim, Y. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b81.cif.gz | 301.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b81.ent.gz | 255.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b81 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b81 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37442.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: Q81B18, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-GOL / #5: 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: 6.8 Å3/Da / Density % sol: 82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MES, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2004 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.81 Å / Num. all: 131796 / Num. obs: 131719 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13005 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→47.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.252 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS was also used for the refinement.
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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 mean: 35.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→47.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.569 Å / Total num. of bins used: 20
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