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- PDB-7xq4: Drimenyl diphosphate synthase from Streptomyces showdoensis (apo) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xq4 | ||||||
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Title | Drimenyl diphosphate synthase from Streptomyces showdoensis (apo) | ||||||
![]() | SQHop_cyclase_C domain-containing protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / Terpene synthases / type II TSs | ||||||
Function / homology | ![]() lanosterol synthase activity / triterpenoid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / lipid droplet / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pan, X.M. / Du, W.Y. / Yang, Q. / Zhang, B. / Dong, L.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery, Structure, and Mechanism of a Class II Sesquiterpene Cyclase. Authors: Pan, X. / Du, W. / Zhang, X. / Lin, X. / Li, F.R. / Yang, Q. / Wang, H. / Rudolf, J.D. / Zhang, B. / 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 | ![]() | 202.9 KB | Display | ![]() |
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PDB format | ![]() | 159.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.5 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xqzC ![]() 7xr7C ![]() 7xraC ![]() 7xruC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 55088.172 Da / Num. of mol.: 1 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: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, NaCl |
-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 30, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→56.96 Å / Num. obs: 70754 / % possible obs: 98.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 16.2 / Num. measured all: 461347 / Scaling rejects: 311 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: The starting model is predicted by Alphafold2 Resolution: 1.58→35.27 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.42 Å2 / Biso mean: 19.0946 Å2 / Biso min: 7.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→35.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -17.5812 Å / Origin y: -5.2988 Å / Origin z: -21.4 Å
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Refinement TLS group | Selection details: all |