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Open data
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Basic information
Entry | Database: PDB / ID: 7ygw | |||||||||
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Title | Crystal structure of the Zn2+-bound EFhd1/Swiprosin-2 | |||||||||
![]() | EF-hand domain-containing protein D1 | |||||||||
![]() | METAL BINDING PROTEIN / EF-hand containing protein / mitochondria | |||||||||
Function / homology | ![]() regulation of cellular hyperosmotic salinity response / calcium ion sensor activity / neuron projection development / mitochondrial inner membrane / calcium ion binding / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Eom, S.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical insights into Zn 2+ -bound EF-hand proteins, EFhd1 and EFhd2. Authors: Mun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Eom, S.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.7 KB | Display | ![]() |
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PDB format | ![]() | 22.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ygvC ![]() 7ygyC ![]() 7cltS S: Starting model for refinement C: citing same article ( |
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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: 14592.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: [GAMGS + EFhd1(69-193)](GAMGS: the cleaved site after GST-TEV tag cleavage) Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 2.5 mM ZnSO4, 25% (w/v) Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28255 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 14577 / % possible obs: 99.5 % / Redundancy: 12.5 % / Biso Wilson estimate: 19.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.72→1.75 Å / Num. unique obs: 685 / CC1/2: 0.774 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CLT Resolution: 1.72→37.96 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.9894 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 22.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→37.96 Å
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Refine LS restraints |
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LS refinement shell |
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