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Yorodumi- PDB-5nc4: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nc4 | ||||||
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Title | Crystal structure of the ferric enterobactin receptor (PfeA) in complex with protochelin from Pseudomonas aeruginosa | ||||||
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 transport / siderophore uptake transmembrane transporter activity / 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: 2.8 Å | ||||||
Authors | Moynie, L. / Naismith, J.H. | ||||||
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 | 5nc4.cif.gz | 289.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nc4.ent.gz | 236.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nc4_validation.pdf.gz | 837.1 KB | Display | wwPDB validaton report |
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Full document | 5nc4_full_validation.pdf.gz | 844.8 KB | Display | |
Data in XML | 5nc4_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 5nc4_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/5nc4 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5nc4 | HTTPS FTP |
-Related structure data
Related structure data | 5m9bC 5mzsC 5nr2C 5outC 6i2jC 6q5eC 6r1fC 5m9k 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-FE / |
#3: Chemical | ChemComp-8T2 / ~{ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.66 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000, ADA, Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→157.35 Å / Num. obs: 26955 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.8→2.813 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 245 / CC1/2: 0.867 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M9K 5m9k Resolution: 2.8→78.68 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.907 / SU B: 34.381 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.345 / 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: 110.265 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→78.68 Å
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Refine LS restraints |
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