+Open data
-Basic information
Entry | Database: PDB / ID: 7x15 | |||||||||
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Title | Crystal structure of MIGA2 LD targeting domain | |||||||||
Components | Mitoguardin 2 | |||||||||
Keywords | LIPID TRANSPORT / MIGA2 / FFAT / LD | |||||||||
Function / homology | Function and homology information Synthesis of PA / mitochondrial fusion / plasma membrane => GO:0005886 / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.852 Å | |||||||||
Authors | Kim, H. / Lee, C. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for mitoguardin-2 mediated lipid transport at ER-mitochondrial membrane contact sites. Authors: Kim, H. / Lee, S. / Jun, Y. / Lee, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x15.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x15.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x15_validation.pdf.gz | 637.9 KB | Display | wwPDB validaton report |
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Full document | 7x15_full_validation.pdf.gz | 641.1 KB | Display | |
Data in XML | 7x15_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7x15_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/7x15 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/7x15 | HTTPS FTP |
-Related structure data
Related structure data | 7x14C 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: 30445.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: miga2, fam73b, zgc:113131 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5BLE2 |
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#2: Chemical | ChemComp-FMT / |
#3: Chemical | ChemComp-PEF / |
#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: 3.9 Å3/Da / Density % sol: 68.43 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 18% SOCKALAN cp5, 100 mM HEPES pH7.0, 300 mM ammonum formate |
-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: 0.9794 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 21478 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.997 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.85→2.9 Å / Num. unique obs: 1055 / CC1/2: 0.786 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.852→47.88 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.29 / 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: 158.2 Å2 / Biso mean: 44.7408 Å2 / Biso min: 6.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.852→47.88 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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