+Open data
-Basic information
Entry | Database: PDB / ID: 8a6u | ||||||
---|---|---|---|---|---|---|---|
Title | PcIDS1 in complex with Mg2+ | ||||||
Components | Isoprenyl diphosphate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Insects / Biosynthesis / Terpenes / Metal regulation / Catalysis | ||||||
Function / homology | Function and homology information pheromone biosynthetic process / dimethylallyltranstransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Phaedon cochleariae (mustard beetle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ecker, F. / Boland, W. / Groll, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat.Chem. / Year: 2023 Title: Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors. Authors: Ecker, F. / Vattekkatte, A. / Boland, W. / Groll, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8a6u.cif.gz | 298.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8a6u.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/8a6u ftp://data.pdbj.org/pub/pdb/validation_reports/a6/8a6u | HTTPS FTP |
---|
-Related structure data
Related structure data | 8a6vC 8a6zC 8a70C 8a73C 8a74C 8a78C 8a7aC 8a7bC 8a7cC 8a7jC 8a7kC 8a7lC 8a7rC 8a7uC 1ubxS 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: 39978.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaedon cochleariae (mustard beetle) / Production host: Escherichia coli (E. coli) / References: UniProt: M1JS91, dimethylallyltranstransferase #2: Chemical | #3: 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: 2.54 Å3/Da / Density % sol: 51.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.2 M MgCl2, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 94381 / % possible obs: 98 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.65→1.75 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 15316 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UBX Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.381 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.16 Å2 / Biso mean: 36.621 Å2 / Biso min: 18.54 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.692 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|