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Open data
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Basic information
Entry | Database: PDB / ID: 8a7a | ||||||
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Title | PcIDS1 in complex with Mg2+ and 3-Br-GPP | ||||||
![]() | Isoprenyl diphosphate synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Insects / Biosynthesis / Terpenes / Metal regulation / Catalysis | ||||||
Function / homology | ![]() pheromone biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ecker, F. / Boland, W. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302 KB | Display | ![]() |
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PDB format | ![]() | 242.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a6uSC ![]() 8a6vC ![]() 8a6zC ![]() 8a70C ![]() 8a73C ![]() 8a74C ![]() 8a78C ![]() 8a7bC ![]() 8a7cC ![]() 8a7jC ![]() 8a7kC ![]() 8a7lC ![]() 8a7rC ![]() 8a7uC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39978.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-L7X / [( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.47 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 100839 / % possible obs: 97.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 33658 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8A6U Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.451 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.077 / 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: 84.5 Å2 / Biso mean: 30.604 Å2 / Biso min: 16.43 Å2
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Refinement step | Cycle: final / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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