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Yorodumi- PDB-6r1f: Crystal structure of the ferric enterobactin receptor mutant R480... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r1f | |||||||||
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Title | Crystal structure of the ferric enterobactin receptor mutant R480A from Pseudomonas aeruginosa (PfeA) in complex with enterobactin | |||||||||
Components | Ferric enterobactin receptor | |||||||||
Keywords | MEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor / protochelin | |||||||||
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 PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å | |||||||||
Authors | Moynie, L. / Naismith, J.H. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model. Authors: Moynie, L. / Milenkovic, S. / Mislin, G.L.A. / Gasser, V. / Malloci, G. / Baco, E. / McCaughan, R.P. / Page, M.G.P. / Schalk, I.J. / Ceccarelli, M. / Naismith, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r1f.cif.gz | 288.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r1f.ent.gz | 236.5 KB | Display | PDB format |
PDBx/mmJSON format | 6r1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/6r1f ftp://data.pdbj.org/pub/pdb/validation_reports/r1/6r1f | HTTPS FTP |
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-Related structure data
Related structure data | 5m9bC 5mzsC 5nc4C 5nr2C 5outC 6i2jC 6q5eSC 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: 78399.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-EB4 / |
#4: 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: 3.48 Å3/Da / Density % sol: 64.7 % |
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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: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→43.51 Å / Num. obs: 19766 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.11→3.16 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 968 / CC1/2: 0.52 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q5E Resolution: 3.11→43.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.927 / SU B: 54.711 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.632 Å2
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Refinement step | Cycle: LAST / Resolution: 3.11→43.51 Å
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Refine LS restraints |
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