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Yorodumi- PDB-8d3i: Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d3i | ||||||||||||
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Title | Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A mutant complexed with quinolin-4-amine | ||||||||||||
Components | (Apoptosis-inducing factor 1, ...) x 2 | ||||||||||||
Keywords | OXIDOREDUCTASE / mitochondrial import / oxidative phosphorylation / SAXS | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / cellular response to aldosterone / positive regulation of necroptotic process / NADH dehydrogenase activity / 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 / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / cellular response to aldosterone / positive regulation of necroptotic process / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / chromosome condensation / response to L-glutamate / 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 / mitochondrial intermembrane space / neuron differentiation / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||||||||
Authors | Brosey, C.A. / Tainer, J.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Integrating early structural selection into chemical library screening for drug discovery with high-throughput small-angle X-ray scattering (SAXS) Authors: Brosey, C.A. / Link, T. / Shen, R. / Moiani, D. / Burnett, K. / Hura, G. / Jones, D.E. / Tainer, J.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d3i.cif.gz | 579 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d3i.ent.gz | 396.2 KB | Display | PDB format |
PDBx/mmJSON format | 8d3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/8d3i ftp://data.pdbj.org/pub/pdb/validation_reports/d3/8d3i | HTTPS FTP |
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-Related structure data
Related structure data | 8d3eC 8d3gC 8d3hC 8d3jC 8d3kC 8d3nC 8d3oC 5kvhS S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.539998331022, -0.84113386077, -0.0299270907284), (-0.841452857521, 0.540320470331, -0.00329816783788), (0.018944420385, 0.0234012308828, -0.999546642898)Vector: 36. ...NCS oper: (Code: given Matrix: (-0.539998331022, -0.84113386077, -0.0299270907284), Vector: |
-Components
-Apoptosis-inducing factor 1, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 59355.434 Da / Num. of mol.: 1 / Mutation: W196A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: O95831, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors |
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#2: Protein | Mass: 59371.434 Da / Num. of mol.: 1 / Mutation: W196A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: O95831, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors |
-Non-polymers , 5 types, 60 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris, pH 8.5, 0.32 M Na2SO4, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→29.49 Å / Num. obs: 37931 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 49.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.04 / Rrim(I) all: 0.135 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.65→2.77 Å / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4578 / CC1/2: 0.865 / Rpim(I) all: 0.287 / Rrim(I) all: 0.969 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KVH Resolution: 2.65→29.49 Å / SU ML: 0.328 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7679 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: 55.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→29.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.495592137127 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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