- PDB-4bv6: Refined crystal structure of the human Apoptosis inducing factor -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4bv6
Title
Refined crystal structure of the human Apoptosis inducing factor
Components
APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
Keywords
OXIDOREDUCTASE / APOPTOSIS / NUCLEAR CHROMATINOLYSIS / DNA BINDING
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 / 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
THIS ENTRY 4BV6 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1M6ISF) ...THIS ENTRY 4BV6 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1M6ISF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I:
Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.57 Å3/Da / Density % sol: 52.25 % Description: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA 1M6I.MTZ DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I. H.YE,C.CANDE,N.C. STEPHANOU, S.JIANG, S.GURBUXANI,N. ...Description: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA 1M6I.MTZ DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I. H.YE,C.CANDE,N.C. STEPHANOU, S.JIANG, S.GURBUXANI,N.LAROCHETTE,E. DAUGAS, C.GARRIDO, G.KROEMER, H.WU
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Wavelength: 1
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Method to determine structure: OTHER / Resolution: 1.8→33.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.574 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 546-557 ARE DISORDERED. AUTHOR USED THE SF DATA FROM ENTRY 1M6I
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21526
2846
6 %
RANDOM
Rwork
0.19389
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obs
0.19518
44509
93.95 %
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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