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Open data
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Basic information
Entry | Database: PDB / ID: 4ayh | ||||||
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Title | The X-ray structure of zinc bound ZinT | ||||||
![]() | METAL-BINDING PROTEIN YODA | ||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() | ||||||
Function / homology | Calycin beta-barrel core domain / ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alaleona, F. / Ilari, A. / Battistoni, A. / Petrarca, P. / Chiancone, E. | ||||||
![]() | ![]() Title: The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc. Authors: Andrea Ilari / Flaminia Alaleona / Giancarlo Tria / Patrizia Petrarca / Andrea Battistoni / Carlotta Zamparelli / Daniela Verzili / Mattia Falconi / Emilia Chiancone / ![]() Abstract: BACKGROUND: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the ...BACKGROUND: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim. METHODS: ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy). RESULTS: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with ...RESULTS: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a KD value of 22±2nM for ZinT, while those with ZnuA point to one high affinity (KD<20nM) and one low affinity Zn(II) binding site (KD in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other. CONCLUSIONS: ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA. GENERAL SIGNIFICANCE: Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 39.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4arhC ![]() 4aw8C ![]() 10ekS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21495.193 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 59.94 % / Description: NONE |
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Crystal grow![]() | pH: 4.6 Details: AMMONIUM SULPHATE 1.5 M, SODIUM ACETATE 0.1 M PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→99 Å / Num. obs: 10654 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 15.02 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.83 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 10EK Resolution: 2.52→50.57 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.851 / SU B: 8.489 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→50.57 Å
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