+Open data
-Basic information
Entry | Database: PDB / ID: 8p1x | ||||||
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Title | TarM(Se)_G117R-UDP-glucose | ||||||
Components | TarM(Se) | ||||||
Keywords | TRANSFERASE / Staphylococcus epidermidis / glycosyltransferase / GT-B fold / alpha-O-glucose / wall teichoic acid | ||||||
Function / homology | TRIETHYLENE GLYCOL / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.03 Å | ||||||
Authors | Guo, Y. / Stehle, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p1x.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p1x.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1x ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1x | HTTPS FTP |
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-Related structure data
Related structure data | 7qd7C 7qh9C 7qntC 8p20C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Staphylococcus epidermidis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 7 types, 300 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.03→49.025 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.068 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.038 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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