+Open data
-Basic information
Entry | Database: PDB / ID: 5ylc | ||||||||||||
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Title | Crystal Structure of MCR-1 Catalytic Domain | ||||||||||||
Components | Probable phosphatidylethanolamine transferase Mcr-1 | ||||||||||||
Keywords | TRANSFERASE / Phosphoethanolamine Transferase / plasmid-mediated transferable colistin resistance gene | ||||||||||||
Function / homology | Function and homology information phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Wei, P.C. / Song, G.J. / Shi, M.Y. / Zhou, Y.F. / Liu, Y. / Lei, J. / Chen, P. / Yin, L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: FASEB J. / Year: 2018 Title: Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance. Authors: Wei, P. / Song, G. / Shi, M. / Zhou, Y. / Liu, Y. / Lei, J. / Chen, P. / Yin, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ylc.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ylc.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ylc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5ylc ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5ylc | HTTPS FTP |
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-Related structure data
Related structure data | 5yleC 5ylfC 4tn0S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37528.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.89 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 10% (v/v) PEG 1000, 5% (v/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.138 Å / Num. obs: 48451 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.03521 / Net I/σ(I): 11.17 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3142 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 4891 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TN0 Resolution: 1.5→33.138 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→33.138 Å
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Refine LS restraints |
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LS refinement shell |
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