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Yorodumi- PDB-7w8y: DMSPP- and Naplha-Me-Trp-bound 6-dimethylallyl tryptophan synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w8y | |||||||||
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Title | DMSPP- and Naplha-Me-Trp-bound 6-dimethylallyl tryptophan synthase, IptA | |||||||||
Components | 6-dimethylallyltryptophan synthase | |||||||||
Keywords | TRANSFERASE / aromatic prenyltransferase / stpreptomyces / secondary metabolites | |||||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / DIMETHYLALLYL S-THIOLODIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / N-methyl-L-tryptophan / 6-dimethylallyltryptophan synthase Function and homology information | |||||||||
Biological species | Streptomyces sp. SN-593 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | |||||||||
Authors | Suemune, H. / Nagano, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w8y.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w8y.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7w8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8y ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8y | HTTPS FTP |
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-Related structure data
Related structure data | 7w8uSC 7w8vC 7w8wC 7w8xC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39726.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SN-593 (bacteria) / Gene: iptA, RVR_4274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6RT90 |
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-Non-polymers , 6 types, 218 molecules
#2: Chemical | ChemComp-DST / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-TRS / |
#5: Chemical | ChemComp-DTT / |
#6: Chemical | ChemComp-E9M / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: HEPES pH7.0, Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→49.12 Å / Num. obs: 57878 / % possible obs: 83.49 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.23 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.39 |
Reflection shell | Resolution: 1.39→1.44 Å / Num. unique obs: 2055 / CC1/2: 0.0503 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W8U Resolution: 1.39→49.12 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.0022 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: 25.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→49.12 Å
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Refine LS restraints |
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LS refinement shell |
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