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Yorodumi- PDB-5miu: G307E variant of Murine Apoptosis Inducing Factor (oxidized state) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5miu | ||||||
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Title | G307E variant of Murine Apoptosis Inducing Factor (oxidized state) | ||||||
Components | Apoptosis-inducing factor 1, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Apoptosis Inducing Factor OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information electron-transferring-flavoprotein dehydrogenase activity / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / oxidoreductase activity, acting on NAD(P)H ...electron-transferring-flavoprotein dehydrogenase activity / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / cellular response to estradiol stimulus / response to ischemia / neuron differentiation / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / neuron apoptotic process / response to oxidative stress / mitochondrial outer membrane / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Sorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / Mastrangelo, E. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural bases of the altered catalytic properties of a pathogenic variant of apoptosis inducing factor. Authors: Sorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / Mastrangelo, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5miu.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5miu.ent.gz | 148.8 KB | Display | PDB format |
PDBx/mmJSON format | 5miu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/5miu ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5miu | HTTPS FTP |
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-Related structure data
Related structure data | 5mivC 3gd3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58400.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aifm1, Aif, Pdcd8 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Z0X1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000,0.2 M sodium acetate, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→48.7 Å / Num. obs: 16448 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.973 / Rrim(I) all: 0.0393 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1197 / CC1/2: 0.735 / Rrim(I) all: 0.1295 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GD3 Resolution: 3.5→48.7 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.943 Å2
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Refinement step | Cycle: 1 / Resolution: 3.5→48.7 Å
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