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- PDB-5miu: G307E variant of Murine Apoptosis Inducing Factor (oxidized state) -

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Basic information

Entry
Database: PDB / ID: 5miu
TitleG307E variant of Murine Apoptosis Inducing Factor (oxidized state)
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / Apoptosis Inducing Factor OXIDOREDUCTASE
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes ...electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / mitochondrial intermembrane space / response to oxidative stress / neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain ...Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / Mastrangelo, E.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural bases of the altered catalytic properties of a pathogenic variant of apoptosis inducing factor.
Authors: Sorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / Mastrangelo, E.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis-inducing factor 1, mitochondrial
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3724
Polymers116,8012
Non-polymers1,5712
Water45025
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1862
Polymers58,4001
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1862
Polymers58,4001
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.040, 110.060, 119.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apoptosis-inducing factor 1, mitochondrial / Programmed cell death protein 8


Mass: 58400.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aifm1, Aif, Pdcd8 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Z0X1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000,0.2 M sodium acetate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3.5→48.7 Å / Num. obs: 16448 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.973 / Rrim(I) all: 0.0393 / Net I/σ(I): 5.3
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1197 / CC1/2: 0.735 / Rrim(I) all: 0.1295 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD3

3gd3


Resolution: 3.5→48.7 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27857 857 5.2 %RANDOM
Rwork0.21175 ---
obs0.21524 15590 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.943 Å2
Baniso -1Baniso -2Baniso -3
1--6.89 Å20 Å20 Å2
2---3.48 Å20 Å2
3---10.37 Å2
Refinement stepCycle: 1 / Resolution: 3.5→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 106 25 7086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197209
X-RAY DIFFRACTIONr_bond_other_d00.026988
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9779760
X-RAY DIFFRACTIONr_angle_other_deg3.639316056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85123.592309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.818151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4591555
X-RAY DIFFRACTIONr_chiral_restr0.0830.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218094
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021639
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2137.1723595
X-RAY DIFFRACTIONr_mcbond_other3.2127.1723594
X-RAY DIFFRACTIONr_mcangle_it5.3910.754485
X-RAY DIFFRACTIONr_mcangle_other5.3910.7494486
X-RAY DIFFRACTIONr_scbond_it3.4867.4153614
X-RAY DIFFRACTIONr_scbond_other3.4857.4153615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.83510.9865276
X-RAY DIFFRACTIONr_long_range_B_refined8.84456.0717853
X-RAY DIFFRACTIONr_long_range_B_other8.84456.0737854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 78 -
Rwork0.347 1111 -
obs--99.66 %

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