+Open data
-Basic information
Entry | Database: PDB / ID: 7ygw | |||||||||
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Title | Crystal structure of the Zn2+-bound EFhd1/Swiprosin-2 | |||||||||
Components | EF-hand domain-containing protein D1 | |||||||||
Keywords | METAL BINDING PROTEIN / EF-hand containing protein / mitochondria | |||||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | |||||||||
Authors | Mun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Eom, S.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Iucrj / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ygw.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ygw.ent.gz | 22.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ygw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ygw_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7ygw_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7ygw_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 7ygw_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/7ygw ftp://data.pdbj.org/pub/pdb/validation_reports/yg/7ygw | HTTPS FTP |
-Related structure data
Related structure data | 7ygvC 7ygyC 7cltS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Efhd1, Sws2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D4J1 | ||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28255 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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