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Yorodumi- PDB-2r0c: Structure of the substrate-free form of the rebeccamycin biosynth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r0c | ||||||
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Title | Structure of the substrate-free form of the rebeccamycin biosynthetic enzyme REBC | ||||||
Components | RebC | ||||||
Keywords | OXIDOREDUCTASE / flavin adenine dinucleotide / Monooxygenase | ||||||
Function / homology | Function and homology information FAD binding / methyltransferase activity / monooxygenase activity / methylation Similarity search - Function | ||||||
Biological species | Lechevalieria aerocolonigenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Ryan, K.S. / Drennan, C.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC Authors: Ryan, K.S. / Howard-Jones, A.R. / Hamill, M.J. / Elliott, S.J. / Walsh, C.T. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0c.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0c.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 2r0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0c ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59927.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria) Strain: ATCC 39243 / Gene: rbmD, rebC / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KI25 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 298 K / pH: 7.4 Details: 1.5 microliters of RebC (9 mg/mL in 150 mM NaCl, 10% glycerol, 25 mM HEPES pH 7.5) were incubated with 0.35 microliters of guanidine-HCl for 30 seconds, followed by addition of 1.5 ...Details: 1.5 microliters of RebC (9 mg/mL in 150 mM NaCl, 10% glycerol, 25 mM HEPES pH 7.5) were incubated with 0.35 microliters of guanidine-HCl for 30 seconds, followed by addition of 1.5 microliters of precipitant solution (19% PEG-8000, 0.1 M HEPES pH 7.4), without mixing, at room temperature and sealed over a precipitant well solution. Immediately after set up, crystal trays were placed on a gel shaker and then, after 12 hours, transferred to a storage space in vibration-isolation. Before being flash-frozen in liquid nitrogen, a crystal was soaked for five seconds in cryogenic solution (19% PEG-8000, 0.1 M HEPES pH 7.4, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.8455, 1.8447, 0.9798 | ||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2006 Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 52005 / % possible obs: 93.9 % / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 25.4 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.458 / % possible all: 67.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 41.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å / Total num. of bins used: 50
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Xplor file |
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