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Yorodumi- PDB-3ept: Structure of the rebeccamycin biosynthetic enzyme RebC with reduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ept | ||||||
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Title | Structure of the rebeccamycin biosynthetic enzyme RebC with reduced flavin | ||||||
Components | RebC | ||||||
Keywords | OXIDOREDUCTASE / flavin / Monooxygenase | ||||||
Function / homology | Function and homology information : / ubiquinone biosynthetic process / FAD binding / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Lechevalieria aerocolonigenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 2.97 Å | ||||||
Authors | Ryan, K.S. / Drennan, C.L. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The FAD cofactor of RebC shifts to an IN conformation upon flavin reduction Authors: Ryan, K.S. / Chakraborty, S. / Howard-Jones, A.R. / Walsh, C.T. / Ballou, D.P. / 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 | 3ept.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ept.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 3ept.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ept_validation.pdf.gz | 911.8 KB | Display | wwPDB validaton report |
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Full document | 3ept_full_validation.pdf.gz | 945.4 KB | Display | |
Data in XML | 3ept_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 3ept_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/3ept ftp://data.pdbj.org/pub/pdb/validation_reports/ep/3ept | HTTPS FTP |
-Related structure data
Related structure data | 2r0gS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 59927.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria) Gene: rbmD, rebC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KI25 #2: Chemical | ChemComp-NA / | #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 51.02 % |
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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. Reduced-RebC was generated by incubating a RebC crystal in a cryogenic solution (19% PEG-8000, 0.1 M HEPES pH 7.4, 20% glycerol) and adding an amount of solid sodium dithionite that is in slight excess of the point at which the crystal became completely clear, indicating that all FAD was reduced. The crystal was then flash-frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9797 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2007 Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→40 Å / Num. obs: 22485 / % possible obs: 90.4 % / Redundancy: 4.1 % / Rsym value: 0.149 |
Reflection shell | Resolution: 2.97→3.08 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 50.7 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 2R0G Resolution: 2.97→40 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Bsol: 10 Å2 / ksol: 0.299767 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.97→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.97→3.02 Å /
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Xplor file |
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