+Open data
-Basic information
Entry | Database: PDB / ID: 6btx | ||||||
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Title | Structure of a bacterial metal transporter | ||||||
Components | Solute carrier family 39 (Iron-regulated transporter) | ||||||
Keywords | METAL TRANSPORT / metal transporter | ||||||
Function / homology | Function and homology information iron ion transmembrane transporter activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Jormakka, M. / Deshpande, C.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Calcium is an essential cofactor for metal efflux by the ferroportin transporter family. Authors: Deshpande, C.N. / Ruwe, T.A. / Shawki, A. / Xin, V. / Vieth, K.R. / Valore, E.V. / Qiao, B. / Ganz, T. / Nemeth, E. / Mackenzie, B. / Jormakka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6btx.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6btx.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 6btx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6btx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6btx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6btx_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6btx_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/6btx ftp://data.pdbj.org/pub/pdb/validation_reports/bt/6btx | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MLJ0 |
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-Non-polymers , 5 types, 11 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-OLC / ( |
#4: Chemical | ChemComp-EDT / {[-( |
#5: Chemical | ChemComp-NI / |
#6: 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: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Tris pH 8.0, 100 mM Na-acetate, 70 mM CaCl2, and 20% PEG500DME |
-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: Aug 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→42.904 Å / Num. obs: 6989 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 57.16 Å2 / Net I/σ(I): 6.29 |
Reflection shell | Resolution: 3.2001→3.3145 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→42.904 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.49 Å2 / Biso mean: 40.98 Å2 / Biso min: 30.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→42.904 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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