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Yorodumi- PDB-4e2l: Crystal Structure of the periplasmic domain of mutant FepE LPS O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e2l | ||||||
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Title | Crystal Structure of the periplasmic domain of mutant FepE LPS O-antigen chain length regulator protein | ||||||
Components | Ferric enterobactin (Enterochelin) transport | ||||||
Keywords | MEMBRANE PROTEIN / FepE polysaccharride co-polymerase / wzz / inner membrane / periplasmic space | ||||||
Function / homology | Function and homology information protein tyrosine kinase activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kalynych, S. / Yao, D. / Magee, J.D. / Cygler, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators. Authors: Kalynych, S. / Yao, D. / Magee, J. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e2l.cif.gz | 413.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e2l.ent.gz | 340.2 KB | Display | PDB format |
PDBx/mmJSON format | 4e2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e2l_validation.pdf.gz | 504.9 KB | Display | wwPDB validaton report |
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Full document | 4e2l_full_validation.pdf.gz | 575.1 KB | Display | |
Data in XML | 4e2l_validation.xml.gz | 77.5 KB | Display | |
Data in CIF | 4e2l_validation.cif.gz | 104.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/4e2l ftp://data.pdbj.org/pub/pdb/validation_reports/e2/4e2l | HTTPS FTP |
-Related 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: 30888.943 Da / Num. of mol.: 9 / Fragment: periplasmic domain / Mutation: delta(258-264) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs0626, fepE, Z0728 / Plasmid: pF04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8 |
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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: 3.46 Å3/Da / Density % sol: 64.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.5M KCl, 0.05M MOPS, 12% (w/v) PEG4K, 20% w/v glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97937 Å |
Detector | Detector: CCD / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.716 Å / Num. obs: 93614 / Observed criterion σ(I): 11.3 / Rsym value: 11.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.716 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 0 / Phase error: 33.62 / 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 / Bsol: 39.268 Å2 / ksol: 0.341 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→49.716 Å
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Refine LS restraints |
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LS refinement shell |
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