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- PDB-7xpi: Structure of a oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 7xpi
TitleStructure of a oxidoreductase
ComponentsApoptosis inducing factor mitochondria associated 2
KeywordsOXIDOREDUCTASE / complex
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / vitamin K metabolic process / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / lipid droplet / flavin adenine dinucleotide binding / mitochondrial outer membrane ...electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / vitamin K metabolic process / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / lipid droplet / flavin adenine dinucleotide binding / mitochondrial outer membrane / positive regulation of apoptotic process / mitochondrion / DNA binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD/NAD(P)-binding domain-containing protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLv, Y. / Sun, Q. / Wang, Q. / Zhu, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into FSP1 catalysis and ferroptosis inhibition.
Authors: Lv, Y. / Liang, C. / Sun, Q. / Zhu, J. / Xu, H. / Li, X. / Li, Y.Y. / Wang, Q. / Yuan, H. / Chu, B. / Zhu, D.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis inducing factor mitochondria associated 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5092
Polymers40,7241
Non-polymers7861
Water4,720262
1
A: Apoptosis inducing factor mitochondria associated 2
hetero molecules

A: Apoptosis inducing factor mitochondria associated 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0184
Polymers81,4472
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area7570 Å2
ΔGint-55 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.376, 113.376, 125.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Apoptosis inducing factor mitochondria associated 2


Mass: 40723.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AIFM2 / Production host: Escherichia coli (E. coli) / References: UniProt: E1BR24
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M (NH4)2SO4, 0.1 M Bis-Tris pH 6.5, 3% w/v PEG 550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32799 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 30.53 Å2 / CC1/2: 0.993 / Net I/σ(I): 621.3
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 3350 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.11 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1617 4.97 %
Rwork0.2 30887 -
obs0.2017 32504 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.24 Å2 / Biso mean: 38.3162 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 2→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 53 262 3098
Biso mean--26.26 40.73 -
Num. residues----363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.060.29311280.2235249498
2.06-2.130.28881240.22862541100
2.13-2.20.2491440.21292533100
2.2-2.290.37121120.2961239893
2.29-2.390.27481450.20892528100
2.39-2.520.26221330.21662578100
2.52-2.680.23381170.20242585100
2.68-2.890.24291280.222583100

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