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- PDB-7fbo: geranyl pyrophosphate C6-methyltransferase BezA binding with S-ad... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fbo | ||||||
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Title | geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine | ||||||
![]() | BezA | ||||||
![]() | TRANSFERASE / methyltransferase geranyl pyrophosphate S-adenosylhomocysteine | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsutsumi, H. / Moriwaki, Y. / Terada, T. / Shimizu, K. / Katsuyama, Y. / Ohnishi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase. Authors: Tsutsumi, H. / Moriwaki, Y. / Terada, T. / Shimizu, K. / Shin-Ya, K. / Katsuyama, Y. / Ohnishi, Y. #1: Journal: J Am Chem Soc / Year: 2018 Title: Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis. Authors: Tsutsumi, H. / Katsuyama, Y. / Izumikawa, M. / Takagi, M. / Fujie, M. / Satoh, N. / Shin-Ya, K. / Ohnishi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.6 KB | Display | ![]() |
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PDB format | ![]() | 143.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 47.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fbhSC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 33605.676 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 25% PEG3350, 0.2 M CH3COONH4. 0.01 M spermine tetrahydrochloride Soaking using 0.1 M HEPES (pH7.5), 35% PEG3350, 1.0 mM SAH. |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50.34 Å / Num. obs: 30941 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.56→2.67 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3824 / CC1/2: 0.835 / Rpim(I) all: 0.33 / Rrim(I) all: 0.926 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7FBH Resolution: 2.56→50.34 Å / SU ML: 0.3289 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.0371 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: 44.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→50.34 Å
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Refine LS restraints |
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LS refinement shell |
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