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Open data
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Basic information
Entry | Database: PDB / ID: 8p1x | ||||||
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Title | TarM(Se)_G117R-UDP-glucose | ||||||
![]() | TarM(Se) | ||||||
![]() | TRANSFERASE / Staphylococcus epidermidis / glycosyltransferase / GT-B fold / alpha-O-glucose / wall teichoic acid | ||||||
Function / homology | TRIETHYLENE GLYCOL / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, Y. / Stehle, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition. Authors: Guo, Y. / Du, X. / Krusche, J. / Beck, C. / Ali, S. / Walter, A. / Winstel, V. / Mayer, C. / Codee, J.D.C. / Peschel, A. / Stehle, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.3 KB | Display | ![]() |
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Full document | ![]() | 769 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qd7C ![]() 7qh9C ![]() 7qntC ![]() 8p20C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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, 1 molecules AAA
#1: Protein | Mass: 59652.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 300 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/UPG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/UPG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UPG / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4. PH range: 6.2-8.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→49.03 Å / Num. obs: 33765 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 15.64 |
Reflection shell | Resolution: 2.03→2.08 Å / Num. unique obs: 2443 / CC1/2: 0.52 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→49.025 Å
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Refine LS restraints |
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LS refinement shell |
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