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Yorodumi- PDB-8r2e: X-ray crystallographic structure of SnoaL2 in complex with the po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r2e | ||||||
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Title | X-ray crystallographic structure of SnoaL2 in complex with the polyketide reaction product | ||||||
Components | SnoL | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis | ||||||
Function / homology | polyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / : / SnoL Function and homology information | ||||||
Biological species | Streptomyces nogalater (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schnell, R. / Schneider, G. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation Authors: Wandi, B.N. / Dinis, P. / Siitonen, V. / Schneider, G. / Schnell, R. / Metsa-Ketele, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r2e.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r2e.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 8r2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2e ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2e | HTTPS FTP |
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-Related structure data
Related structure data | 8r20C 8r2bC 8r2jC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16913.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal His6-tag used in affinity purification / Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoL / Plasmid: pBAD Details (production host): N-terminal His6-tag, not removable Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9RN64 #2: Chemical | ChemComp-XN8 / | Mass: 588.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32O13 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 39 % / Description: rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 25% PEG3350, ligand at 2 mM |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.77 Å / Num. obs: 19854 / % possible obs: 96.7 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 52.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.07 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1348 / CC1/2: 0.529 / Rpim(I) all: 0.583 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.44 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.172 / 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: 33.125 Å2
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Refinement step | Cycle: 1 / Resolution: 2→36 Å
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Refine LS restraints |
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