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Open data
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Basic information
Entry | Database: PDB / ID: 8itq | ||||||
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Title | Terpene cyclase AriE mutant - D128A | ||||||
![]() | Terpene synthase | ||||||
![]() | METAL BINDING PROTEIN / Class I Terpene cyclase | ||||||
Function / homology | Lyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene synthase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | He, J.Y. / Yang, Q. / Dong, L.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of cis-eunicellane synthase AriE from Amycolatopsis arida Authors: Yang, Q. / He, J.Y. / Dong, L.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.9 KB | Display | ![]() |
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PDB format | ![]() | 129.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422 KB | Display | ![]() |
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Full document | ![]() | 424.9 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Components
#1: Protein | Mass: 42459.113 Da / Num. of mol.: 1 / Mutation: D128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1000mM Potassium sodium tartrate, 100mM Imidazole/Hydrochloric acid pH8.0, 200mM Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97851 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→83.9 Å / Num. obs: 36523 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 0.996 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.07→2.13 Å / Num. unique obs: 2796 / CC1/2: 0.991 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold2 Resolution: 2.07→36.77 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 17.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→36.77 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.1231 Å / Origin y: -28.7501 Å / Origin z: -18.0531 Å
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Refinement TLS group | Selection details: all |