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- PDB-8d3e: Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d3e | ||||||||||||
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Title | Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A mutant complexed with 6-fluoroquinolin-4-amine | ||||||||||||
![]() | Apoptosis-inducing factor 1, mitochondrial | ||||||||||||
![]() | OXIDOREDUCTASE / mitochondrial import / oxidative phosphorylation / SAXS | ||||||||||||
Function / homology | ![]() 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 / chromosome condensation / oxidoreductase activity, acting on NAD(P)H ...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 / chromosome condensation / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitochondrial respiratory chain complex I assembly / 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 / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Brosey, C.A. / Tainer, J.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Authors: Brosey, C.A. / Link, T.M. / Shen, R. / Moiani, D. / Burnett, K. / Hura, G.L. / Jones, D.E. / Tainer, J.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 595 KB | Display | ![]() |
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PDB format | ![]() | 408.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d3gC ![]() 8d3hC ![]() 8d3iC ![]() 8d3jC ![]() 8d3kC ![]() 8d3nC ![]() 8d3oC ![]() 5kvhS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.541170844665, -0.840435404371, -0.028327512515), (-0.840725993789, 0.54145340102, -0.00283158797341), (0.0177177947772, 0.0222833032555, -0.999594684932)Vector: -36. ...NCS oper: (Code: given Matrix: (-0.541170844665, -0.840435404371, -0.028327512515), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59355.434 Da / Num. of mol.: 2 / Mutation: W196A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O95831, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 362 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/QDI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QDI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-QDI / | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7-8, 0.3 M Na2SO4, 16-18% PEG3350 / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→29.34 Å / Num. obs: 50201 / % possible obs: 99.3 % / Redundancy: 10.6 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.38→2.46 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4275 / CC1/2: 0.852 / Rpim(I) all: 0.232 / Rrim(I) all: 0.765 / % possible all: 93 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5KVH Resolution: 2.38→29.34 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5811 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: 47.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→29.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.497721391979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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