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- PDB-7ffa: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ffa | ||||||
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Title | Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis | ||||||
![]() | Type III polyketide synthase | ||||||
![]() | TRANSFERASE / diarylpentanoid / type-III polyketide synthase | ||||||
Function / homology | polyketide biosynthetic process / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase-like / Type III polyketide synthase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morita, H. / Wong, C.P. / Liu, Q. / Kodama, T. / Lee, Y. / Nakashima, Y. | ||||||
![]() | ![]() Title: Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. ...Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. / Tu, P.F. / Shi, S.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.2 KB | Display | ![]() |
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PDB format | ![]() | 128.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ffcC ![]() 7ffgC ![]() 7ffhC ![]() 7ffiC ![]() 4yjyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 46877.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris, pH8.5, 0.12M KF, 4% butanediol, 24% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→42.65 Å / Num. obs: 56395 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3896 / CC1/2: 0.869 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YJY Resolution: 1.98→42.65 Å / SU ML: 0.2385 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4664 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 36.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→42.65 Å
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Refine LS restraints |
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LS refinement shell |
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