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Open data
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Basic information
Entry | Database: PDB / ID: 8ki5 | |||||||||
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Title | PhmA, a type I diterpene synthase without NST/DTE motif | |||||||||
![]() | PhmA | |||||||||
![]() | BIOSYNTHETIC PROTEIN / diterpene synthase | |||||||||
Function / homology | (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, B. / Ge, H.M. / Zhu, A. / Zhang, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Biosynthesis of Platelet Activating Factor Antagonist Phomactins Revealing a New Class of Type I Diterpene Synthase Authors: Zhang, L. / Zhang, B. / Zhu, A. / Liu, S.H. / Wu, R. / Zhang, X. / Xu, Z.R. / Ge, H.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 | ![]() | 179.2 KB | Display | ![]() |
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PDB format | ![]() | 143.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.3 KB | Display | ![]() |
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Full document | ![]() | 858.6 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kihC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37484.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FOH / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion / pH: 5.6 Details: 1.0 M Lithium sulfate, 0.1 M Sodium citrate pH 5.6, 0.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→54.38 Å / Num. obs: 23328 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.01→2.06 Å / Num. unique obs: 1705 / CC1/2: 0.808 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→29.23 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: -36.1527 Å / Origin y: -10.5867 Å / Origin z: -9.215 Å
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Refinement TLS group | Selection details: all |