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- PDB-7cav: Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cav | |||||||||
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Title | Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP) | |||||||||
![]() | cis-prenyltransferase MM_0014 | |||||||||
![]() | TRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / Isoprenoid / MM_0014 / archaea / farnesylglycerol | |||||||||
Function / homology | DIMETHYLALLYL DIPHOSPHATE / DIPHOSPHATE / Chem-FQ0 / PHOSPHATE ION![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Unno, H. / Hemmi, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. Authors: Okada, M. / Unno, H. / Emi, K.I. / Matsumoto, M. / Hemmi, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.5 KB | Display | ![]() |
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PDB format | ![]() | 299.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7caqSC ![]() 7carC ![]() 7casC ![]() 7cc3C 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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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 25688.492 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 513 molecules ![](data/chem/img/DMA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FQ0.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FQ0.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DMA / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-FQ0 / #5: Chemical | ChemComp-DPO / #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | The Genebank accession number is 24771896 for the protein. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol, 3 mM farnesyl pyrophosphate (FPP), 0.3 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→48.46 Å / Num. obs: 147512 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 0.688 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 2.05 / Num. unique obs: 7217 / CC1/2: 0.688 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CAQ Resolution: 1.91→47.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.029 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: 42.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→47.92 Å
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Refine LS restraints |
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LS refinement shell |
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