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Yorodumi- PDB-5zzu: Crystal structure of the C-terminal periplasmic domain of EcEptC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zzu | ||||||
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Title | Crystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli- complex with Zn | ||||||
Components | Phosphoethanolamine transferase EptC | ||||||
Keywords | TRANSFERASE / Phosphoethanolamine transferases | ||||||
Function / homology | Function and homology information phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhao, Y.Q. / Cheng, W. / Gu, Y.J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli Authors: Zhao, Y.Q. / Lai, Y.J. / Zhou, D. / Dou, C. / Gu, Y.J. / Nie, C.L. / Wei, Y.Q. / Cheng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zzu.cif.gz | 241.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zzu.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/5zzu ftp://data.pdbj.org/pub/pdb/validation_reports/zz/5zzu | HTTPS FTP |
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-Related structure data
Related structure data | 5znv S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 46005.461 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eptC, cptA, yijP, b3955, JW3927 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0CB39, Transferases; Transferring phosphorus-containing groups #2: Chemical | #3: 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: 1.84 Å3/Da / Density % sol: 33.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium formate (pH7.5), 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Mar 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.83 Å / Num. obs: 56697 / % possible obs: 98.72 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.03 / Rrim(I) all: 0.094 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5219 / CC1/2: 0.887 / Rpim(I) all: 0.196 / Rrim(I) all: 0.472 / % possible all: 90.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZNV 5znv Resolution: 2.1→46.83 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.83 Å
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Refine LS restraints |
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LS refinement shell |
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