+Open data
-Basic information
Entry | Database: PDB / ID: 8a7r | ||||||
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Title | PcIDS1_I420A in complex with Mg2+ and GPP | ||||||
Components | Isoprenyl diphosphate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Insects / Biosynthesis / Terpenes / Metal regulation / Catalysis | ||||||
Function / homology | Function and homology information pheromone biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Phaedon cochleariae (mustard beetle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ecker, F. / Boland, W. / Groll, M. | ||||||
Funding support | Germany, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a7r.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a7r.ent.gz | 226.8 KB | Display | PDB format |
PDBx/mmJSON format | 8a7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/8a7r ftp://data.pdbj.org/pub/pdb/validation_reports/a7/8a7r | HTTPS FTP |
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-Related structure data
Related structure data | 8a6uSC 8a6vC 8a6zC 8a70C 8a73C 8a74C 8a78C 8a7aC 8a7bC 8a7cC 8a7jC 8a7kC 8a7lC 8a7uC 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, 2 molecules AB
#1: Protein | Mass: 39936.887 Da / Num. of mol.: 2 / Mutation: I420A 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 |
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-Non-polymers , 5 types, 137 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-MES / | #4: Chemical | ChemComp-GPP / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.2 CaCl2, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 51160 / % possible obs: 96.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7097 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8A6U Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.249 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.95 Å2 / Biso mean: 34.131 Å2 / Biso min: 19.06 Å2
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Refinement step | Cycle: final / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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