+Open data
-Basic information
Entry | Database: PDB / ID: 2isk | ||||||
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Title | BluB bound to flavin anion (charge transfer complex) | ||||||
Components | BluB | ||||||
Keywords | FLAVOPROTEIN / oxidoreductase / flavin / monooxygenase / flavin destructase / vitamin B12 / dithionite / charge transfer complex | ||||||
Function / homology | Function and homology information aerobic 5,6-dimethylbenzimidazole synthase / 5,6-dimethylbenzimidazole synthase activity / cobalamin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / nucleotide binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Larsen, N.A. / Taga, M.E. / Howard-Jones, A.R. / Walsh, C.T. / Walker, G.C. | ||||||
Citation | Journal: Nature / Year: 2007 Title: BluB cannibalizes flavin to form the lower ligand of vitamin B12. Authors: Taga, M.E. / Larsen, N.A. / Howard-Jones, A.R. / Walsh, C.T. / Walker, G.C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Sinorhizobium meliloti bluB is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B12. | ||||||
History |
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Remark 600 | HETEROGEN THE FLAVIN IS IN THE ANION STATE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isk.cif.gz | 371.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isk.ent.gz | 303.1 KB | Display | PDB format |
PDBx/mmJSON format | 2isk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isk ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The assembly consists of a homodimer. There are four homodimers in the assymetric unit. Dimer 1 = chain A/B, Dimer 2 = chain C/D, Dimer 3 = chain E/F, Dimer 4 = chain G/H |
-Components
#1: Protein | Mass: 25820.369 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: bluB / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q92PC8 #2: Chemical | ChemComp-FNR / #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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.8 M Ammonium Sulfate, 100 mM Citrate soaked in saturated dithionite prior to freezing, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9919 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 94174 / Num. obs: 94174 / % possible obs: 84.6 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.1 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.9919 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Xplor file |
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