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- PDB-6fbo: Human Methionine Adenosyltransferase II mutant (S114A) in I222 cr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fbo | ||||||
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Title | Human Methionine Adenosyltransferase II mutant (S114A) in I222 crystal form | ||||||
![]() | S-adenosylmethionine synthase isoform type-2 | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
![]() | ![]() Title: Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory beta subunit and quinolone-based compounds. Authors: Panmanee, J. / Bradley-Clarke, J. / Mato, J.M. / O'Neill, P.M. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.1 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fbnC ![]() 6fbpC ![]() 6fcbC ![]() 6fcdC ![]() 6g6rC ![]() 5a1iS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43704.625 Da / Num. of mol.: 1 / Mutation: S114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 231 molecules ![](data/chem/img/PPK.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PPK / ( | ||||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ADN / | #6: Chemical | ChemComp-PG4 / | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% PEG600 0.1M HEPES pH.7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→58.28 Å / Num. obs: 34507 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.119 / Rrim(I) all: 0.208 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.766 / Num. unique obs: 2037 / CC1/2: 0.782 / Rpim(I) all: 0.538 / Rrim(I) all: 0.94 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A1I Resolution: 1.8→58.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.776 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→58.28 Å
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Refine LS restraints |
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