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Yorodumi- PDB-5out: CRYSTAL STRUCTURE OF THE FERRIC ENTEROBACTIN RECEPTOR (PFEA) MUTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5out | ||||||
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Title | CRYSTAL STRUCTURE OF THE FERRIC ENTEROBACTIN RECEPTOR (PFEA) MUTANT (G324V) FROM PSEUDOMONAS AERUGINOSA | ||||||
Components | Ferric enterobactin receptor | ||||||
Keywords | MEMBRANE PROTEIN / PfeA / TBDT | ||||||
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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 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 | 5out.cif.gz | 279.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5out.ent.gz | 235.9 KB | Display | PDB format |
PDBx/mmJSON format | 5out.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5out_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 5out_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 5out_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5out_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/5out ftp://data.pdbj.org/pub/pdb/validation_reports/ou/5out | HTTPS FTP |
-Related structure data
Related structure data | 5m9bC 5mzsC 5nc4C 5nr2C 6i2jC 6q5eC 6r1fC 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: 78527.203 Da / Num. of mol.: 1 / Mutation: G324V 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: 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: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: PEG 8000 ADA Magnesium acetate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→39.08 Å / Num. obs: 19876 / % possible obs: 80.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.377 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.669 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Resolution: 2.9→39.08 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.88 / SU B: 57.47 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.496 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→39.08 Å
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Refine LS restraints |
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