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- PDB-3gd3: Crystal structure of a naturally folded murine apoptosis inducing... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gd3 | ||||||
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Title | Crystal structure of a naturally folded murine apoptosis inducing factor | ||||||
![]() | (Apoptosis-inducing factor 1, mitochondrial) x 2 | ||||||
![]() | OXIDOREDUCTASE / alpha and beta protein / Acetylation / Apoptosis / DNA-binding / FAD / Flavoprotein / Mitochondrion / Nucleus / Phosphoprotein / Transit peptide | ||||||
Function / homology | ![]() 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 / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / response to L-glutamate ...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 / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / response to L-glutamate / NADH dehydrogenase activity / apoptotic mitochondrial changes / 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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sevrioukova, I.F. | ||||||
![]() | ![]() Title: Redox-linked conformational dynamics in apoptosis-inducing factor Authors: Sevrioukova, I.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 746.1 KB | Display | ![]() |
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PDB format | ![]() | 624.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gd4C ![]() 1gv4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58328.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | Sequence details | THE AUTHOR STATES THAT CHAINS E AND F ARE LIKELY PARTS OF THE N-TERMINI OF CHAINS A,B,C, AND D. 48- ...THE AUTHOR STATES THAT CHAINS E AND F ARE LIKELY PARTS OF THE N-TERMINI OF CHAINS A,B,C, AND D. 48-49 N-TERMINAL RESIDUES IN ALL FOUR MOLECULES IN THE ASYMMETRIC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 7 Details: 15% PEG 4000, 0.35M KNO3, pH 7.0, microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2008 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→408.25 Å / Num. all: 61080 / Num. obs: 49548 / % possible obs: 81.12 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.97 % / Rmerge(I) obs: 0.174 / Rsym value: 0.174 |
Reflection shell | Resolution: 2.8→2.873 Å / Redundancy: 5.06 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.715 / % possible all: 69.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GV4 Resolution: 2.95→46.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.907 / SU B: 47.252 / SU ML: 0.415 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.017 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→46.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / 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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