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- PDB-5ynw: 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: 5ynw | |||||||||
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Title | Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with DMASPP and 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 | ![]() | 148.2 KB | Display | ![]() |
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PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016.2 KB | Display | ![]() |
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Full document | ![]() | 1022 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 43.9 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
-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 , 5 types, 543 molecules ![](data/chem/img/DST.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/8XL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/8XL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-8XL / | #5: Chemical | ChemComp-IMD / | #6: 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: 56.09 % / Mosaicity: 1.255 ° |
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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: 1.94→25 Å / Num. obs: 57870 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.057 / Rrim(I) all: 0.133 / Χ2: 1.094 / Net I/σ(I): 14.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 122.25 Å2 / Biso mean: 33.737 Å2 / Biso min: 18.38 Å2
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Refinement step | Cycle: final / Resolution: 1.95→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.953→2.003 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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