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- PDB-5ynu: Crystal structure of an aromatic prenyltransferase FAMD1 from Fis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ynu | ||||||
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Title | Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with INN | ||||||
![]() | aromatic prenyltransferase | ||||||
![]() | TRANSFERASE / prenyltransferase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, J. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
![]() | ![]() Title: Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis. Authors: Wang, J. / Chen, C.C. / Yang, Y. / Liu, W. / Ko, T.P. / Shang, N. / Hu, X. / Xie, Y. / Huang, J.W. / Zhang, Y. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.4 KB | Display | ![]() |
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PDB format | ![]() | 234.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499 KB | Display | ![]() |
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Full document | ![]() | 502.7 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36988.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ambP3 / Plasmid: pET-28a / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 763 molecules ![](data/chem/img/8XL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-POP / | #6: Chemical | ChemComp-DMA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % / Mosaicity: 0.486 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 8, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→25 Å / Num. obs: 90097 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.026 / Rrim(I) all: 0.052 / Χ2: 0.959 / Net I/σ(I): 15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.03 Å2 / Biso mean: 26.176 Å2 / Biso min: 12.42 Å2
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Refinement step | Cycle: final / Resolution: 1.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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