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Open data
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Basic information
Entry | Database: PDB / ID: 6oz6 | ||||||
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Title | Crystal structure of MraY bound to 3'-hydroxymureidomycin A | ||||||
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![]() | MEMBRANE PROTEIN/TRANSFERASE / peptidoglycan biosynthesis / antibiotic target / integral membrane enzyme / translocase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TRANSFERASE complex | ||||||
Function / homology | ![]() phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / identical protein binding ...phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mashalidis, E.H. / Lee, S.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Chemical logic of MraY inhibition by antibacterial nucleoside natural products. Authors: Mashalidis, E.H. / Kaeser, B. / Terasawa, Y. / Katsuyama, A. / Kwon, D.Y. / Lee, K. / Hong, J. / Ichikawa, S. / Lee, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 613.3 KB | Display | ![]() |
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PDB format | ![]() | 511.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6oyhC ![]() 6oyzC ![]() 5ckrS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 15057.651 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 40954.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: VF5 / Gene: mraY, aq_053 / Variant: VF5 / Production host: ![]() ![]() References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.88 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 20% polyethylene glycol, 0.2 M ammonium thiocyanate, 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→73.717 Å / Num. obs: 31974 / % possible obs: 91.15 % / Redundancy: 15.4 % / CC1/2: 0.971 / Net I/σ(I): 3.55 |
Reflection shell | Resolution: 3.7→3.832 Å / Num. unique obs: 2414 / CC1/2: 0.664 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CKR Resolution: 3.7→73.717 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→73.717 Å
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Refine LS restraints |
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LS refinement shell |
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