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Yorodumi- PDB-5tsb: Crystal structure of the Zrt-/Irt-like protein from Bordetella br... -
+Open data
-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+ | ||||||
Components | Membrane protein | ||||||
Keywords | METAL BINDING PROTEIN / ZIP / transporter / zinc / cadmium / lipidic cubic phase / binuclear metal center / membrane protein | ||||||
Function / homology | Zinc/iron permease / ZIP Zinc transporter / metal ion transmembrane transporter activity / zinc ion transport / plasma membrane / : / Zinc transporter ZIPB Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Zhang, T. / Fellner, M. / Sui, D. / Liu, J. / Hu, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tsb.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tsb.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 5tsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/5tsb ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5tsb | 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: 31618.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) (bacteria) Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Plasmid: pLW01 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) pLysS / References: UniProt: A0A0H3LM39 | ||
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#2: Chemical | ChemComp-CD / #3: 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: 2.48 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→26.494 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.2
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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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