+Open data
-Basic information
Entry | Database: PDB / ID: 7w8v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | DMSPP- and 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 / TRYPTOPHAN / 6-dimethylallyltryptophan synthase Function and homology information | |||||||||
Biological species | Streptomyces sp. SN-593 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Suemune, H. / Nagano, S. / Tomoya, H. | |||||||||
Funding support | Japan, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7w8v.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7w8v.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7w8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8v ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8v | HTTPS FTP |
---|
-Related structure data
Related structure data | 7w8uSC 7w8wC 7w8xC 7w8yC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#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 |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|