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- PDB-7kjf: Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and neridronate -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kjf | ||||||
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Title | Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and neridronate | ||||||
![]() | epi-isozizaene synthase | ||||||
![]() | LYASE / terpene cyclase / complex / bisphosphonate inhibitor / risedronate | ||||||
Function / homology | ![]() epi-isozizaene synthase / epi-isozizaene synthase activity / Lyases; Carbon-oxygen lyases; Acting on phosphates / terpene synthase activity / lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ronnebaum, T.A. / Gardner, S.M. / Christianson, D.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An Aromatic Cluster in the Active Site of epi -Isozizaene Synthase Is an Electrostatic Toggle for Divergent Terpene Cyclization Pathways. Authors: Ronnebaum, T.A. / Gardner, S.M. / Christianson, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.5 KB | Display | ![]() |
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PDB format | ![]() | 119.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kj8C ![]() 7kj9C ![]() 7kjdC ![]() 7kjeC ![]() 7kjgC ![]() 3kb9S 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43716.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A6M9XZI2, UniProt: Q9K499*PLUS, epi-isozizaene synthase |
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-Non-polymers , 5 types, 237 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NRD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NRD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-NRD / ( | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.05 mM Bis-Tris, pH 5.5, 0.05 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 27% PEG3350, 0.01 M L-Proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 4, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.76 Å / Num. obs: 69464 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.37 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 3544 / CC1/2: 0.559 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3KB9 Resolution: 1.4→45.16 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8854 / Stereochemistry target values: GeoStd + Monomer Library
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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: 17.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.16 Å
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Refine LS restraints |
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LS refinement shell |
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