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Open data
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Basic information
Entry | Database: PDB / ID: 5wa3 | ||||||
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Title | Pyridine synthase, TbtD, from thiomuracin biosynthesis | ||||||
![]() | Pyridine synthase TbtD | ||||||
![]() | BIOSYNTHETIC PROTEIN / pyridine synthase / Diels-Alder / thiopeptide / thiomuracin | ||||||
Function / homology | Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / Thiopeptide-type bacteriocin biosynthesis domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cogan, D.P. / Nair, S.K. | ||||||
![]() | ![]() Title: Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Authors: Cogan, D.P. / Hudson, G.A. / Zhang, Z. / Pogorelov, T.V. / van der Donk, W.A. / Mitchell, D.A. / Nair, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w98SC ![]() 5w99C ![]() 5wa4C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40320.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51 Gene: Tbis_0552 / Plasmid: pRARE / Production host: ![]() ![]() Sequence details | TbtD in the NCBI database: WP_050760415.1 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.4 M NaH2PO4, 1 M KH2PO4 pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→55.08 Å / Num. obs: 34569 / % possible obs: 93.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W98 Resolution: 2.8→104.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.451 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.271 / 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: 88.879 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→104.52 Å
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Refine LS restraints |
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