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- PDB-5aym: Crystal structure of a bacterial homologue of iron transporter fe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aym | ||||||
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Title | Crystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state with soaked iron | ||||||
![]() | Solute carrier family 39 (Iron-regulated transporter) | ||||||
![]() | TRANSPORT PROTEIN / alpha helical | ||||||
Function / homology | Ferroportin-1 / Ferroportin1 (FPN1) / iron ion transmembrane transporter activity / MFS transporter superfamily / metal ion binding / plasma membrane / : / Ferreportin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Taniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Ishitani, R. / Jormakka, M. / Nureki, O. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.3 KB | Display | ![]() |
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Full document | ![]() | 425.6 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE2 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.5 Details: 100 mM Tris, pH 7.5, 50-200 mM K-formate, 50-100 mM (NH4)2HPO4, and 26-32% PEG550MME, 5 mM FeSO4 soaked |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.2 Å / Num. obs: 18454 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 10.4 |
Reflection shell | Rejects: 0 |
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Processing
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Refinement | Resolution: 3→49.157 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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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: 71.37 Å2 / Biso mean: 26.7089 Å2 / Biso min: 7.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.157 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: 13 / % reflection obs: 100 %
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