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Yorodumi- PDB-5ayn: Crystal structure of a bacterial homologue of iron transporter fe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ayn | ||||||
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Title | Crystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state | ||||||
Components | Solute carrier family 39 (Iron-regulated transporter) | ||||||
Keywords | TRANSPORT PROTEIN / alpha helical | ||||||
Function / homology | Ferroportin-1 / Ferroportin1 (FPN1) / iron ion transmembrane transporter activity / MFS transporter superfamily / metal ion binding / plasma membrane / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Ferreportin Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.202 Å | ||||||
Authors | Taniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Ishitani, R. / Jormakka, M. / Nureki, O. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin Authors: Taniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Wada, M. / Ito, K. / Ishitani, R. / Jormakka, M. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ayn.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayn.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ayn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayn ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayn | HTTPS FTP |
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-Related 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: 48600.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: slc39, Bd2019 / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q6MLJ0 | ||
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#2: Chemical | ChemComp-K / | ||
#3: Chemical | ChemComp-OLC / ( #4: 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: 2.39 Å3/Da / Density % sol: 48.47 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8.5 Details: 100 mM Tris, pH 8.5, 100 mM NaK-tartrate, 100 mM KNO3, 30% PEG550MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2014 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.404 Å / Num. obs: 24182 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 10.6 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.202→48.404 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.79 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.55 Å2 / Biso mean: 33.3048 Å2 / Biso min: 15.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.202→48.404 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
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