+Open data
-Basic information
Entry | Database: PDB / ID: 8a7b | ||||||
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Title | PcIDS1_D319N in complex with Mg2+ and 3-Br-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: 1.65 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 | 8a7b.cif.gz | 293.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a7b.ent.gz | 236.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/8a7b ftp://data.pdbj.org/pub/pdb/validation_reports/a7/8a7b | HTTPS FTP |
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-Related structure data
Related structure data | 8a6uSC 8a6vC 8a6zC 8a70C 8a73C 8a74C 8a78C 8a7aC 8a7cC 8a7jC 8a7kC 8a7lC 8a7rC 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: 39977.977 Da / Num. of mol.: 2 / Mutation: D319N 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, 324 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CO3 / | #5: Chemical | ChemComp-L7X / [( | #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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.2 M MgCl2, 25% 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: 0.92 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 94379 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.65→1.75 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14986 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8A6U Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.181 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 75.58 Å2 / Biso mean: 27.985 Å2 / Biso min: 15.53 Å2
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Refinement step | Cycle: final / Resolution: 1.65→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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