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Yorodumi- PDB-4r82: Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SgcE6 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r82 | ||||||
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Title | Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SgcE6 in complex with NAD and FAD fragments | ||||||
Components | Oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro | ||||||
Function / homology | Function and homology information FAD reductase (NADH) / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / FMN binding Similarity search - Function | ||||||
Biological species | Streptomyces globisporus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.659 Å | ||||||
Authors | Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor ...Title: Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus. Authors: Chang, C.Y. / Lohman, J.R. / Cao, H. / Tan, K. / Rudolf, J.D. / Ma, M. / Xu, W. / Bingman, C.A. / Yennamalli, R.M. / Bigelow, L. / Babnigg, G. / Yan, X. / Joachimiak, A. / Phillips, G.N. / Shen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r82.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r82.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 4r82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r82_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4r82_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4r82_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4r82_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r82 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r82 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19968.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces globisporus (bacteria) / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8GME2 |
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-Non-polymers , 7 types, 252 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-MG / | #7: Chemical | #8: 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: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M calcium acetate, 0.1M MES:NaCl, 20% (w/v) PEG8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2012 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→35 Å / Num. all: 43097 / Num. obs: 43097 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2 / Num. unique all: 2089 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.659→34.928 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.659→34.928 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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