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- PDB-3vc2: Crystal structure of geranyl diphosphate C-methyltransferase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vc2 | ||||||
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Title | Crystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor A3(2) in complex with Mg2+, geranyl diphosphate, and S-adenosyl-L-homocysteine | ||||||
![]() | Geranyl diphosphate 2-C-methyltransferase | ||||||
![]() | TRANSFERASE / Rossmann fold / methyltransferase fold / SAM-dependent methyltransferase / C-methyltransferase / terpenoid biosynthesis / 2-methylisoborneol biosynthesis | ||||||
Function / homology | ![]() geranyl diphosphate 2-C-methyltransferase / C-methyltransferase activity / terpene metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / methylation / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koksal, M. / Christianson, D.W. | ||||||
![]() | ![]() Title: Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification. Authors: Koksal, M. / Chou, W.K. / Cane, D.E. / Christianson, D.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 676.1 KB | Display | ![]() |
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PDB format | ![]() | 556.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 125.9 KB | Display | |
Data in CIF | ![]() | 170.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vc1SC 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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12 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 35040.090 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9F1Y5, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 1186 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/GPP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/GPP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SAH / #4: Chemical | ChemComp-GPP / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-Tris (pH 6.5), 25% polyethylene glycol 3350, 200 mM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011 Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.046→50 Å / Num. all: 263284 / Num. obs: 246191 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.046→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.1 / Num. unique all: 24533 / Rsym value: 0.574 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VC1 Resolution: 2.046→48.891 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 23.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.236 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.046→48.891 Å
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Refine LS restraints |
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LS refinement shell |
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