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Open data
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Basic information
Entry | Database: PDB / ID: 8gy0 | |||||||||
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Title | Agrocybe pediades linalool sunthase (Ap.LS) | |||||||||
![]() | Terpene synthase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / Monoterpene synthase | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Rehka, T. / Sharma, D. / Lin, F. / Lim, C. / Choong, Y.K. / Chacko, J. / Zhang, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Understanding of Fungal Terpene Synthases for the Formation of Linear or Cyclic Terpene Products. Authors: T, R. / Sharma, D. / Lin, F. / Choong, Y.K. / Lim, C. / Jobichen, C. / Zhang, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.8 KB | Display | ![]() |
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PDB format | ![]() | 107.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ps1S ![]() 2wbuS S: Starting model for refinement |
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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
#1: Protein | Mass: 37439.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A8H4VHP2, Lyases; Carbon-oxygen lyases; Acting on phosphates #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 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: 1.98→50 Å / Num. obs: 48065 / % possible obs: 90.5 % / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.98→2.01 Å / Num. unique obs: 1368 / Rsym value: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ps1, 2wbu Resolution: 1.988→46.804 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.291 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.206 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.281 Å2
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Refinement step | Cycle: LAST / Resolution: 1.988→46.804 Å
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Refine LS restraints |
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LS refinement shell |
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