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Open data
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Basic information
Entry | Database: PDB / ID: 7w8v | |||||||||
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Title | DMSPP- and Trp-bound 6-dimethylallyl tryptophan synthase, IptA | |||||||||
![]() | 6-dimethylallyltryptophan synthase | |||||||||
![]() | TRANSFERASE / aromatic prenyltransferase / stpreptomyces / secondary metabolites | |||||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / 6-dimethylallyltryptophan synthase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Suemune, H. / Nagano, S. / Tomoya, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of a 6-dimethylallyltryptophan synthase, IptA: Insights into substrate tolerance and enhancement of prenyltransferase activity. Authors: Suemune, H. / Nishimura, D. / Mizutani, K. / Sato, Y. / Hino, T. / Takagi, H. / Shiozaki-Sato, Y. / Takahashi, S. / Nagano, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.5 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w8uSC ![]() 7w8wC ![]() 7w8xC ![]() 7w8yC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 39726.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-DST / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-TRP / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: HPEPES pH7.5, Ammoniumu Sulfate |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→49.3 Å / Num. obs: 44406 / % possible obs: 95.82 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.926 / Net I/σ(I): 7.68 |
Reflection shell | Resolution: 1.61→1.671 Å / Num. unique obs: 4317 / CC1/2: 0.569 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7W8U Resolution: 1.61→49.3 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1405 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→49.3 Å
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Refine LS restraints |
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LS refinement shell |
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