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- PDB-7y88: class I diterpene synthase (CyS-GGPP-Mg2+) from Streptomyces cattleya -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y88 | ||||||
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Title | class I diterpene synthase (CyS-GGPP-Mg2+) from Streptomyces cattleya | ||||||
![]() | Putative glutamate dehydrogenase/leucine dehydrogenase | ||||||
![]() | BIOSYNTHETIC PROTEIN / class I diterpene synthase (CyS-GGPP-Mg2+) / Streptomyces cattleya | ||||||
Function / homology | terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / GERANYLGERANYL DIPHOSPHATE / Putative glutamate dehydrogenase/leucine dehydrogenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xing, B. / Ma, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Authors: Xing, B. / Xu, H. / Li, A. / Lou, T. / Xu, M. / Wang, K. / Xu, Z. / Dickschat, J.S. / Yang, D. / Ma, 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 | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y50SC ![]() 7y87C 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 on special symmetry positions |
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Components
#1: Protein | Mass: 42050.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057 Gene: SCATT_p16530 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-GRG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1000 mM Sodium citrate tribasic and 100 mM Sodium cacodylate / Hydrochloric acid pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→56.57 Å / Num. obs: 32571 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.87→1.91 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 3231 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7Y50 Resolution: 1.87→43.753 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.61 / 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: 71.6 Å2 / Biso mean: 25.2424 Å2 / Biso min: 9.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→43.753 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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