+Open data
-Basic information
Entry | Database: PDB / ID: 6noi | ||||||
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Title | Crystal structure of Tsn15 in apo form | ||||||
Components | Tsn15 | ||||||
Keywords | LYASE / cyclase / tetronasin | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION Function and homology information | ||||||
Biological species | Streptomyces longisporoflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Little, R. / Paiva, F.C.R. / Dias, M.V.B. / Leadlay, P. | ||||||
Citation | Journal: Nat Catal / Year: 2019 Title: Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis Authors: Little, R. / Paiva, F.C.R. / Jenkins, R. / Hong, H. / Sun, Y. / Demydchuk, Y. / Samborskyy, M. / Tosin, M. / Leeper, F.J. / Dias, M.V.B. / Leadlay, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6noi.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6noi.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 6noi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6noi ftp://data.pdbj.org/pub/pdb/validation_reports/no/6noi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22880.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces longisporoflavus (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-PEG / | #5: 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: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTP pH 6, 25% PEG 1500 buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→29.7 Å / Num. obs: 38365 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 22.7 / Num. measured all: 239481 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→29.699 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.56 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.41 Å2 / Biso mean: 22.7645 Å2 / Biso min: 7.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→29.699 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 24.9135 Å / Origin y: 20.1143 Å / Origin z: 65.6429 Å
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Refinement TLS group |
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