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- PDB-5wa4: Pyridine synthase, TbtD, from thiomuracin biosynthesis bound to a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wa4 | ||||||
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Title | Pyridine synthase, TbtD, from thiomuracin biosynthesis bound to an N-terminal leader peptide fragment | ||||||
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![]() | BIOSYNTHETIC PROTEIN / pyridine synthase / Diels-Alder / thiopeptide / thiomuracin | ||||||
Function / homology | Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / Uncharacterized protein / 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 | ![]() | 379 KB | Display | ![]() |
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PDB format | ![]() | 310.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 525.7 KB | Display | ![]() |
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Full document | ![]() | 569.7 KB | Display | |
Data in XML | ![]() | 67.4 KB | Display | |
Data in CIF | ![]() | 92.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w98SC ![]() 5w99C ![]() 5wa3C 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.: 6 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 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 1825.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Sequence details | TbtD matches to NCBI Reference Sequence: WP_050760415.1 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M magnesium formate and 17.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07809 Å / Relative weight: 1 |
Reflection | Resolution: 2.646→23.127 Å / Num. obs: 76366 / % possible obs: 98.9 % / Redundancy: 13.3 % / Net I/σ(I): 15.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W98 Resolution: 2.646→48.048 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.52 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.646→48.048 Å
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Refine LS restraints |
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LS refinement shell |
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