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- PDB-1y6g: alpha-glucosyltransferase in complex with UDP and a 13_mer DNA co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y6g | ||||||
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Title | alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution | ||||||
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![]() | TRANSFERASE/DNA / ![]() | ||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lariviere, L. / Sommer, N. / Morera, S. | ||||||
![]() | ![]() Title: Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase. Authors: Lariviere, L. / Sommer, N. / Morera, 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 | ![]() | 191.7 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1xv5C ![]() 1y6fSC ![]() 1y8zC ![]() 1ya6C C: citing same article ( S: Starting model for refinement |
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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
-DNA chain , 2 types, 2 molecules CD
#1: DNA chain | Mass: 4030.647 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3652.402 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 2 molecules AB
#3: Protein | ![]() Mass: 47041.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 90 molecules ![](data/chem/img/NCO.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NCO / #5: Chemical | ![]() #6: Chemical | ChemComp-CL / | ![]() #7: Chemical | ChemComp-EDO / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.4 % | ||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 10000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 25, 2004 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→20 Å / Num. all: 23702 / Num. obs: 23542 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 69 Å2 / Rsym value: 0.087 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1Y6F Resolution: 2.8→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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