+Open data
-Basic information
Entry | Database: PDB / ID: 2r0g | ||||||
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Title | Chromopyrrolic acid-soaked RebC with bound 7-carboxy-K252c | ||||||
Components | RebC | ||||||
Keywords | OXIDOREDUCTASE / flavin adenine dinucleotide / chromopyrrolic acid / 7-carboxy-K252c / 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 / MOLECULAR REPLACEMENT / Resolution: 2.37 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 | 2r0g.cif.gz | 222.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0g.ent.gz | 175 KB | Display | PDB format |
PDBx/mmJSON format | 2r0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0g_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2r0g_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2r0g_validation.xml.gz | 43 KB | Display | |
Data in CIF | 2r0g_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0g ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0g | HTTPS FTP |
-Related structure data
Related structure data | 2r0cSC 2r0pC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) 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 #2: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.5 microliters of RebC (9 mg/mL in 150 mM NaCl, 10% glycerol, 25 mM HEPES pH 7.5) was 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) was 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. A crystal was then soaked in 19% PEG-8000, 0.1 M HEPES pH 7.4, and 5 mM chromopyrrolic acid for 1 week. The crystal was then soaked for 5 seconds in a cryogenic solution containing 19% PEG-8000, 0.1 M HEPES pH 7.4, 20% glycerol, and 5 mM chromopyrrolic acid and then flash-frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 141.4 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50 Å / Num. all: 46328 / Num. obs: 46328 / % possible obs: 90.8 % / Redundancy: 6.2 % / Rsym value: 0.054 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.37→2.45 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 3138 / Rsym value: 0.274 / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2R0C Resolution: 2.37→50 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.37→50 Å
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Refine LS restraints |
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