+Open data
-Basic information
Entry | Database: PDB / ID: 6nnw | ||||||
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Title | Tsn15 in complex with substrate intermediate | ||||||
Components | Tetronasin | ||||||
Keywords | UNKNOWN FUNCTION / Complex / cyclase | ||||||
Function / homology | Chem-KUJ / PHOSPHATE ION / PROPANOIC ACID Function and homology information | ||||||
Biological species | Streptomyces longisporoflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Paiva, F.C.R. / Little, R. / Leadlay, P. / Dias, M.V.B. | ||||||
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 | 6nnw.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nnw.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/6nnw ftp://data.pdbj.org/pub/pdb/validation_reports/nn/6nnw | HTTPS FTP |
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-Related structure data
Related structure data | 6noiSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22693.400 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-PO4 / | #4: Chemical | ChemComp-PPI / | #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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 27 % PEG 1500 and 0,1 M PCPT pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976247 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976247 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.7→44.46 Å / Num. obs: 45895 / % possible obs: 98.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Net I/σ(I): 13 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NOI Resolution: 1.7→44.456 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.16 Å2 / Biso mean: 29.0717 Å2 / Biso min: 9.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→44.456 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: 17
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Refinement TLS params. | Method: refined / Origin x: -26.0305 Å / Origin y: -1.5022 Å / Origin z: 21.7549 Å
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Refinement TLS group |
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