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- PDB-6ix5: The structure of LepI complex with SAM and its substrate analogue -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ix5 | ||||||
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Title | The structure of LepI complex with SAM and its substrate analogue | ||||||
![]() | O-methyltransferase lepI | ||||||
![]() | BIOSYNTHETIC PROTEIN / Leporin / SAM / O-methyltransferase / Pericyclase | ||||||
Function / homology | ![]() : / : / O-methyltransferase activity / secondary metabolite biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cai, Y. / Ohashi, M. / Hai, Y. / Tang, Y. / Zhou, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI. Authors: Cai, Y. / Hai, Y. / Ohashi, M. / Jamieson, C.S. / Garcia-Borras, M. / Houk, K.N. / Zhou, J. / Tang, 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 | ![]() | 202.5 KB | Display | ![]() |
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PDB format | ![]() | 156.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 64.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ix3SC ![]() 6ix7C ![]() 6ix8C ![]() 6ix9C 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, 2 molecules AB
#1: Protein | Mass: 45491.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167 Gene: lepI, AFLA_066940 / Production host: ![]() ![]() References: UniProt: B8NJH3, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 8 types, 959 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/B0L.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B0L.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / | #7: Chemical | #8: Chemical | ChemComp-IMD / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1M Magnesium chloride hexahydrate, 0.1M ADA(pH 6.5), 12%(w/v) PEG 6000 |
-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: May 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 114325 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.876 / Num. unique obs: 5721 / CC1/2: 0.809 / Rpim(I) all: 0.368 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IX3 Resolution: 1.7→34.987 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.55 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34.987 Å
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Refine LS restraints |
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LS refinement shell |
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