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- PDB-5fs8: Crystal structure of the G308E mutant of human apoptosis inducing... -

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Basic information

Entry
Database: PDB / ID: 5fs8
TitleCrystal structure of the G308E mutant of human apoptosis inducing factor
ComponentsAPOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / MITOCHONDRIA / FLAVOPROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / mitochondrial respiratory chain complex assembly / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / mitochondrial respiratory chain complex assembly / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / cellular response to nitric oxide / response to ischemia / cellular response to estradiol stimulus / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / neuron differentiation / positive regulation of neuron apoptotic process / cellular response to hypoxia / protein dimerization activity / mitochondrial inner membrane / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / Pyridine nucleotide-disulphide oxidoreductase / 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 ...Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / Pyridine nucleotide-disulphide oxidoreductase / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSevrioukova, I.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure/Function Relations in Aifm1 Variants Associated with Neurodegenerative Disorders
Authors: Sevrioukova, I.
History
DepositionDec 31, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1252
Polymers56,3391
Non-polymers7861
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 89.750, 60.330
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL / PROGRAMMED CELL DEATH PROTEIN 8 / APOPTOSIS INDUCING FACTOR


Mass: 56339.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 103-613 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ADDITIONAL C-TERMINAL RESIDUES L614-V615-P616-R617 ARE PART OF THE THROMBIN SITE. RESIDUES 104-124,546-558 AND 612-617 ARE DISORDERED
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O95831, 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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG308E MUTATION AND ADDITIONAL L614-V615-P616-R617 RESIDUES AT THE C-TERMINUS

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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: 2.45 Å3/Da / Density % sol: 49.75 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M AMMONIUM ACETATE AND 20% POLY-ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→37.17 Å / Num. obs: 102452 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6I

1m6i


Resolution: 1.4→89.75 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.34 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19247 5075 5 %RANDOM
Rwork0.16443 ---
obs0.16583 97342 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.382 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.41 Å2
2--0.55 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.4→89.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 53 644 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194044
X-RAY DIFFRACTIONr_bond_other_d0.0010.023957
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9815523
X-RAY DIFFRACTIONr_angle_other_deg0.78339145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20123.277177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34315726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3511537
X-RAY DIFFRACTIONr_chiral_restr0.0880.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214617
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02929
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_it1.2161.4191988
X-RAY DIFFRACTIONr_mcbond_other1.2161.4181987
X-RAY DIFFRACTIONr_mcangle_it1.9972.1232506
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6411.6442056
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6632.3762991
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 308 -
Rwork0.322 6235 -
obs--83.94 %
Refinement TLS params.Method: refined / Origin x: -5.597 Å / Origin y: 4.217 Å / Origin z: -29.5551 Å
111213212223313233
T0.0064 Å20.0015 Å2-0.0112 Å2-0.0042 Å2-0.0026 Å2--0.0571 Å2
L0.3256 °20.1216 °2-0.0594 °2-0.3593 °20.0004 °2--0.923 °2
S-0.0114 Å °0.0043 Å °-0.005 Å °0.0221 Å °0.0293 Å °0.0081 Å °0.041 Å °-0.0347 Å °-0.0179 Å °

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