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- PDB-7zc3: Crystal structure of human copper chaperone Atox1 bound to zinc i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zc3 | ||||||
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Title | Crystal structure of human copper chaperone Atox1 bound to zinc ion by CxxC motif | ||||||
![]() | Copper transport protein ATOX1 | ||||||
![]() | CHAPERONE / Copper Transport Protein / Metallochaperone / Atox1 Protein / Metal Ions / Zinc | ||||||
Function / homology | ![]() metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / response to oxidative stress / copper ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mangini, V. / Belviso, B.D. / Arnesano, F. / Caliandro, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the Human Copper Chaperone ATOX1 Bound to Zinc Ion. Authors: Mangini, V. / Belviso, B.D. / Nardella, M.I. / Natile, G. / Arnesano, F. / Caliandro, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.2 KB | Display | ![]() |
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PDB format | ![]() | 30.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qotS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 7412.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): BL21(DE3) / References: UniProt: O00244 #2: Chemical | ChemComp-ZN / | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.21 % / Description: Needle-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Drop:12.5mg/ml Atox1 + 1.62mM ZnSO4 in 25mM Sodium Phosphate buffer pH 7.0, 2mM DTT; Reservoir: 1.9M Li2SO4, 100mM MES pH 6.0, 2.5% glycerol; VAPOR DIFFUSION, SITTING DROP, temperature 293K. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 12, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.04 Å / Num. obs: 23876 / % possible obs: 94.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 887 / CC1/2: 0.765 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4qot Resolution: 1.9→25.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.34 / Stereochemistry target values: ML
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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: 98.78 Å2 / Biso mean: 32.4581 Å2 / Biso min: 15.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→25.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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