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Yorodumi- PDB-6i98: Structure of the ferrioxamine B transporter FoxA from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i98 | ||||||
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Title | Structure of the ferrioxamine B transporter FoxA from Pseudomonas aeruginosa, apo state | ||||||
Components | Ferric hydroxamate uptake | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information siderophore transport / siderophore uptake transmembrane transporter activity / outer membrane / cell outer membrane / signaling receptor activity / cell surface receptor signaling pathway Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Josts, I. / Tidow, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Elife / Year: 2019 Title: Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake. Authors: Josts, I. / Veith, K. / Tidow, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i98.cif.gz | 278.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i98.ent.gz | 232.5 KB | Display | PDB format |
PDBx/mmJSON format | 6i98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i98_validation.pdf.gz | 1012.8 KB | Display | wwPDB validaton report |
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Full document | 6i98_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6i98_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6i98_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/6i98 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/6i98 | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75421.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: fhuA, fhuA_5, C0044_18480, CAZ10_13360, CCBH4851_00003, DZ940_30305, EGY23_22030, PAERUG_E15_London_28_01_14_03466 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CQY7, UniProt: Q9I116*PLUS |
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-Non-polymers , 7 types, 40 molecules
#2: Chemical | ChemComp-NI / | ||||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-C8E / ( #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | #8: 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: 5.24 Å3/Da / Density % sol: 76.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium sulfate, 0.1M HEPES pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.03332 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.53 Å / Num. obs: 40394 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.092 / Rrim(I) all: 0.226 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.91 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4492 / CC1/2: 0.547 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→151.17 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 24.424 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141 Å2 / Biso mean: 58.049 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.8→151.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.7742 Å / Origin y: -70.3826 Å / Origin z: -12.8859 Å
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