+Open data
-Basic information
Entry | Database: PDB / ID: 6oyh | ||||||
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Title | Crystal structure of MraY bound to carbacaprazamycin | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/TRANSFERASE / peptidoglycan biosynthesis / antibiotic target / integral membrane enzyme / translocase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TRANSFERASE complex | ||||||
Function / homology | Function and homology information 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 | Lama glama (llama) Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Mashalidis, E.H. / Lee, S.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oyh.cif.gz | 997.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oyh.ent.gz | 854 KB | Display | PDB format |
PDBx/mmJSON format | 6oyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oyh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6oyh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6oyh_validation.xml.gz | 62.6 KB | Display | |
Data in CIF | 6oyh_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/6oyh ftp://data.pdbj.org/pub/pdb/validation_reports/oy/6oyh | HTTPS FTP |
-Related structure data
Related structure data | 6oyzC 6oz6C 5ckrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 40954.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: mraY, aq_053 / Production host: Escherichia coli (E. coli) References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase #3: Chemical | ChemComp-NK4 / ( #4: Water | ChemComp-HOH / | |
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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: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 22% polyethylene glycol 4000, 0.2 M potassium 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→43.941 Å / Num. obs: 61002 / % possible obs: 98.7 % / Redundancy: 4.3 % / CC1/2: 0.892 / Rpim(I) all: 0.07917 / Net I/σ(I): 12.86 |
Reflection shell | Resolution: 2.95→3.055 Å / Num. unique obs: 5579 / CC1/2: 0.444 / Rpim(I) all: 0.636 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CKR Resolution: 2.95→43.941 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.92 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→43.941 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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