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- PDB-5cgm: Structure of Mycobacterium thermoresistibile GlgE in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cgm | |||||||||
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Title | Structure of Mycobacterium thermoresistibile GlgE in complex with maltose at 1.95A resolution | |||||||||
![]() | Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | |||||||||
![]() | TRANSFERASE / GlgE / Maltose / GH13 / maltosyltransferase | |||||||||
Function / homology | ![]() starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L. | |||||||||
![]() | ![]() Title: Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism. Authors: Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 303.8 KB | Display | ![]() |
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PDB format | ![]() | 239 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 57.8 KB | Display | |
Data in CIF | ![]() | 85.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cimC ![]() 5cj5C ![]() 3zssS 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 / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 77618.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: glgE, KEK_12948 / Production host: ![]() ![]() References: UniProt: G7CL00, starch synthase (maltosyl-transferring) #2: Polysaccharide | |
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-Non-polymers , 9 types, 981 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PEG / #10: Chemical | ChemComp-EDO / #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 300, sodium phosphate-citrate, maltose / PH range: 4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.95→37.74 Å / Num. obs: 147668 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZSS Resolution: 1.95→19.66 Å / Cor.coef. Fo:Fc: 0.9269 / Cor.coef. Fo:Fc free: 0.9089 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.111
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Displacement parameters | Biso mean: 32.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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