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Yorodumi- PDB-6bpo: The crystal structure of the Ferric-Catecholate import receptor F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bpo | ||||||
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Title | The crystal structure of the Ferric-Catecholate import receptor Fiu from K12 E. coli: Closed form (P1) | ||||||
Components | Catecholate siderophore receptor Fiu | ||||||
Keywords | MEMBRANE PROTEIN / Ferric-Catecholate / TonB-Dependent Receptor / Membrane Transport / Antibiotic Uptake / Iron Transporter | ||||||
Function / homology | Function and homology information microcin transport / siderophore-dependent iron import into cell / siderophore uptake transmembrane transporter activity / siderophore transport / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Grinter, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: The structure of the bacterial iron-catecholate transporter Fiu suggests that it imports substrates via a two-step mechanism. Authors: Grinter, R. / Lithgow, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bpo.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6bpo.ent.gz | 900.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/6bpo ftp://data.pdbj.org/pub/pdb/validation_reports/bp/6bpo | HTTPS FTP |
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-Related structure data
Related structure data | 6bpmC 6bpnC 5fp1S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 78415.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fiu, ybiL, b0805, JW0790 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: P75780 #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bis-Tris Propane, 20 % PEG3350, 0.2 M Na-Malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50.31 Å / Num. obs: 116009 / % possible obs: 99 % / Observed criterion σ(I): 1.1 / Redundancy: 3.7 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.151 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.199 / Num. unique obs: 5714 / CC1/2: 0.491 / Rpim(I) all: 0.802 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FP1 Resolution: 2.9→29.23 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.851 / SU R Cruickshank DPI: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.448 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.301
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Displacement parameters | Biso mean: 56.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→29.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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