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Yorodumi- PDB-3gd4: Crystal structure of the reduced, NAD-bound form of murine apopto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gd4 | ||||||
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Title | Crystal structure of the reduced, NAD-bound form of murine apoptosis inducing factor | ||||||
Components | Apoptosis-inducing factor 1, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta protein / Acetylation / Apoptosis / DNA-binding / FAD / Flavoprotein / Mitochondrion / Nucleus / Phosphoprotein / Transit peptide | ||||||
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: 2.24 Å | ||||||
Authors | Sevrioukova, I.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Redox-linked conformational dynamics in apoptosis-inducing factor Authors: Sevrioukova, I.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gd4.cif.gz | 367.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gd4.ent.gz | 299 KB | Display | PDB format |
PDBx/mmJSON format | 3gd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gd4 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gd4 | HTTPS FTP |
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-Related structure data
Related structure data | 3gd3C 1gv4S 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 55579.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aif, Aifm1, Pdcd8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z0X1 #2: Chemical | #3: Chemical | #4: 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: 2.907345 Å3/Da / Density % sol: 57.693363 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG 4000, 10% isopropanol, 0.1 M Li citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2398 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2002 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→30.67 Å / Num. all: 60034 / Num. obs: 57099 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.036 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.57 / Num. unique all: 4363 / Rsym value: 0.367 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GV4 Resolution: 2.24→30.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.78 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.228 / ESU R Free: 0.187 / 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: 46.368 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→30.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.298 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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