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Yorodumi- PDB-6ipw: Crystal structure of CqsB2 from Streptomyces exfoliatus in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ipw | ||||||
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Title | Crystal structure of CqsB2 from Streptomyces exfoliatus in complex with the product, 1-(2-hydroxypropyl)-2-methyl-carbazole-3,4-dione | ||||||
Components | CqsB2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Carbazole biosynthesis / polyketide aromatase/cyclase | ||||||
Function / homology | START-like domain superfamily / Chem-AO6 / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptomyces exfoliatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tomita, T. / Kobayashi, M. / Nishiyama, M. / Kuzuyama, T. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces. Authors: Kobayashi, M. / Tomita, T. / Shin-Ya, K. / Nishiyama, M. / Kuzuyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipw.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipw.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ipw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ipw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6ipw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ipw_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6ipw_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipw ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipw | HTTPS FTP |
-Related structure data
Related structure data | 6ipvSC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27645.105 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RILCodonPlus / References: UniProt: A0A5A4PV77*PLUS #2: Chemical | ChemComp-AO6 / #3: Water | ChemComp-HOH / | Sequence details | The sequence has been deposited to DDBJ with accession code LC406090. | |
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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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl (pH8.5), 30% (w/v) PEG 4000, 0.2M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→125.43 Å / Num. obs: 61403 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.035 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.543 / Num. unique obs: 3009 / CC1/2: 0.948 / Rpim(I) all: 0.145 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IPV Resolution: 2.1→125.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.613 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.664 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→125.43 Å
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Refine LS restraints |
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