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- PDB-3vmq: Crystal structure of Staphylococcus aureus membrane-bound transgl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vmq | ||||||
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Title | Crystal structure of Staphylococcus aureus membrane-bound transglycosylase: Apoenzyme | ||||||
![]() | Monofunctional glycosyltransferase | ||||||
![]() | TRANSFERASE / Transmembrane / Glycosyltransferase / Bacterial cell wall synthesis / Membrane | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, C.Y. / Shih, H.W. / Lin, L.Y. / Tien, Y.W. / Cheng, T.J.R. / Cheng, W.C. / Wong, C.H. / Ma, C. | ||||||
![]() | ![]() Title: Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism Authors: Huang, C.Y. / Shih, H.W. / Lin, L.Y. / Tien, Y.W. / Cheng, T.J.R. / Cheng, W.C. / Wong, C.H. / Ma, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.3 KB | Display | ![]() |
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PDB format | ![]() | 154.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 464.4 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vmrC ![]() 3vmsC ![]() 3vmtC ![]() 3fwlS ![]() 3fwm ![]() 3hzsS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30314.369 Da / Num. of mol.: 2 / Fragment: residues 28-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q99T05, Transferases; Glycosyltransferases #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100mM MgCl2, 100mM HEPES, 25% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30.079 Å / Num. obs: 23658 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.5→2.59 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HZS, 3FWM, 3FWL Resolution: 2.518→30.079 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8011 / SU ML: 0.32 / σ(F): 0.02 / Phase error: 25.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.035 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 294.13 Å2 / Biso mean: 80.3988 Å2 / Biso min: 20.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.518→30.079 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -24.3479 Å / Origin y: 1.2705 Å / Origin z: -5.0863 Å
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Refinement TLS group |
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