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Yorodumi- PDB-6bpm: The crystal structure of the Ferric-Catecholate import receptor F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bpm | ||||||
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Title | The crystal structure of the Ferric-Catecholate import receptor Fiu from K12 E. coli: Closed form (C21) | ||||||
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: 2.5 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 | 6bpm.cif.gz | 574.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bpm.ent.gz | 470.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/6bpm ftp://data.pdbj.org/pub/pdb/validation_reports/bp/6bpm | HTTPS FTP |
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-Related structure data
Related structure data | 6bpnC 6bpoC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 78415.461 Da / Num. of mol.: 2 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: Chemical | ChemComp-POG / ( #3: Sugar | #4: 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: 2.9 Å3/Da / Density % sol: 57.6 % / Description: Diamond Plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 3350, 4% Polypropylene Glycol P400, 0.2 M NaCl, 0.1 M Tris |
-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 | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.35 Å / Num. obs: 68066 / % possible obs: 100 % / Observed criterion σ(I): 1.1 / Redundancy: 3.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.147 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.56→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.026 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4585 / CC1/2: 0.536 / Rpim(I) all: 0.95 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FP1 Resolution: 2.5→49.345 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.345 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -33.5148 Å / Origin y: 36.83 Å / Origin z: 30.1927 Å
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Refinement TLS group | Selection details: all |