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Yorodumi- PDB-6z2n: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z2n | ||||||
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Title | Crystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV-L6 | ||||||
Components | Ferric enterobactin receptor | ||||||
Keywords | MEMBRANE PROTEIN / TONB dependent transporter / siderophore | ||||||
Function / homology | Function and homology information enterobactin transmembrane transporter activity / enterobactin transport / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / siderophore transport / outer membrane / enterobactin binding / cell outer membrane / signaling receptor activity Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.029 Å | ||||||
Authors | Naismith, J.H. / Moynie, L.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2022 Title: Hijacking of the Enterobactin Pathway by a Synthetic Catechol Vector Designed for Oxazolidinone Antibiotic Delivery in Pseudomonas aeruginosa. Authors: Moynie, L. / Hoegy, F. / Milenkovic, S. / Munier, M. / Paulen, A. / Gasser, V. / Faucon, A.L. / Zill, N. / Naismith, J.H. / Ceccarelli, M. / Schalk, I.J. / Mislin, G.L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z2n.cif.gz | 277.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z2n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/6z2n ftp://data.pdbj.org/pub/pdb/validation_reports/z2/6z2n | HTTPS FTP |
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-Related structure data
Related structure data | 5nc3C 6y47C 6yy5C 6z33C 7obwC 6q5eS 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: 78744.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-Q5N / |
#4: Chemical | ChemComp-FE / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: PEG 8000, ADA, Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 3.029→86.24 Å / Num. obs: 21109 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 3.03→3.08 Å / Num. unique obs: 1019 / CC1/2: 0.485 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6q5e Resolution: 3.029→75.66 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.93 / SU B: 50.249 / SU ML: 0.373 / Cross valid method: NONE / ESU R Free: 0.42 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.234 Å2
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Refinement step | Cycle: LAST / Resolution: 3.029→75.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -83.213 Å / Origin y: 26.9742 Å / Origin z: 95.2489 Å
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Refinement TLS group | Selection: ALL |