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Open data
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Basic information
Entry | Database: PDB / ID: 6oyz | ||||||
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Title | Crystal structure of MraY bound to capuramycin | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 603.2 KB | Display | ![]() |
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PDB format | ![]() | 500.7 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 ![]() 6oz6C ![]() 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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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, ![]() #3: Chemical | ChemComp-NKM / ( | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.42 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 18% polyethylene glycol 4000, 0.4 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 PILATUS 6M-F / Detector: PIXEL / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.62→87.64 Å / Num. obs: 32765 / % possible obs: 99.95 % / Redundancy: 15.2 % / CC1/2: 0.989 / Net I/σ(I): 10.25 |
Reflection shell | Resolution: 3.62→3.749 Å / Num. unique obs: 3244 / CC1/2: 0.343 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5CKR Resolution: 3.62→87.637 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.62→87.637 Å
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Refine LS restraints |
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LS refinement shell |
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