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- PDB-5tsb: Crystal structure of the Zrt-/Irt-like protein from Bordetella br... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tsb | ||||||
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Title | Crystal structure of the Zrt-/Irt-like protein from Bordetella bronchiseptica with bound Cd2+ | ||||||
![]() | Membrane protein | ||||||
![]() | METAL BINDING PROTEIN / ZIP / transporter / zinc / cadmium / lipidic cubic phase / binuclear metal center / membrane protein | ||||||
Function / homology | Zinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / : / Zinc transporter ZIPB![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, T. / Fellner, M. / Sui, D. / Liu, J. / Hu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway. Authors: Zhang, T. / Liu, J. / Fellner, M. / Zhang, C. / Sui, D. / Hu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.6 KB | Display | ![]() |
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PDB format | ![]() | 37.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.6 KB | Display | ![]() |
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Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 12.4 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31618.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Plasmid: pLW01 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % / Mosaicity: 0.529 ° |
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Crystal grow | Temperature: 294 K / Method: lipidic cubic phase / pH: 7.5 Details: protein concentration: 15 mg/mL; buffer: 10 mM Hepes pH 7.3, 300 mM NaCl, 5% Glycerol, 0.02% DDM; crystallization condition: 0.1 M Sodium chloride, 0.1 M Cadmium chloride hemi, 0.1 M Tris-HCl pH 7.5, 33% PEG 400 |
-Data collection
Diffraction | Mean temperature: 193 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→26.494 Å / Num. obs: 7889 / % possible obs: 93.2 % / Redundancy: 10.1 % / Biso Wilson estimate: 53.74 Å2 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.048 / Rrim(I) all: 0.169 / Χ2: 1.132 / Net I/av σ(I): 17.4 / Net I/σ(I): 4.6 / Num. measured all: 79447 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.17 Å2 / Biso mean: 48.1683 Å2 / Biso min: 16.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→26.494 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: 5
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