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- PDB-3oeq: Crystal structure of trimeric frataxin from the yeast Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 3oeq
TitleCrystal structure of trimeric frataxin from the yeast Saccharomyces cerevisiae, with full length n-terminus
ComponentsFrataxin homolog, mitochondrial
KeywordsTRANSPORT PROTEIN / ALPHA/BETA SANDWICH / METALLOCHAPERONE / IRON-STORAGE
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / Complex III assembly / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / heme biosynthetic process / iron-sulfur cluster assembly / response to iron(II) ion ...Mitochondrial iron-sulfur cluster biogenesis / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / Complex III assembly / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / heme biosynthetic process / iron-sulfur cluster assembly / response to iron(II) ion / ferroxidase / ferroxidase activity / glutathione metabolic process / ferric iron binding / iron ion transport / ferrous iron binding / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / response to oxidative stress / intracellular iron ion homeostasis / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
Frataxin/CyaY / Frataxin / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...Frataxin/CyaY / Frataxin / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Frataxin homolog, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSoderberg, C.A.G. / Rajan, S. / Gakh, O. / Ta, C. / Isaya, G. / Al-Karadaghi, S.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering.
Authors: Soderberg, C.A. / Shkumatov, A.V. / Rajan, S. / Gakh, O. / Svergun, D.I. / Isaya, G. / Al-Karadaghi, S.
#1: Journal: Structure / Year: 2006
Title: The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron
Authors: Karlberg, T. / Schagerlof, U. / Gakh, O. / Park, S. / Ryde, U. / Lindahl, M. / Lleath, K. / Garman, E. / Isaya, G. / Al-Karadaghi, S.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frataxin homolog, mitochondrial


Theoretical massNumber of molelcules
Total (without water)13,6711
Polymers13,6711
Non-polymers00
Water00
1
A: Frataxin homolog, mitochondrial

A: Frataxin homolog, mitochondrial

A: Frataxin homolog, mitochondrial


Theoretical massNumber of molelcules
Total (without water)41,0143
Polymers41,0143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.360, 121.360, 121.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Frataxin homolog, mitochondrial / Frataxin homolog intermediate form


Mass: 13671.182 Da / Num. of mol.: 1 / Fragment: UNP residues 52-174 / Mutation: Y73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YFH1, YDL120W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07540

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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: 5.45 Å3/Da / Density % sol: 77.42 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.7 M (NH4)2SO4, 0.2 M Li2SO4, 4 % -butyrolactone, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 5, 2008
RadiationMonochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.96→30 Å / Num. obs: 6002 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.6
Reflection shellResolution: 2.96→3.03 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.54 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQL

2fql


Resolution: 2.96→28.6 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.87 / SU B: 38.897 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.362
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.29235 617 9.7 %RANDOM
Rwork0.26581 ---
all0.26838 5714 --
obs0.26838 5714 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.164 Å2
Refinement stepCycle: LAST / Resolution: 2.96→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 0 0 931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022951
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9871299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9945120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.77826.74443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.93115157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.808152
X-RAY DIFFRACTIONr_chiral_restr0.1190.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021724
X-RAY DIFFRACTIONr_mcbond_it0.2531.5605
X-RAY DIFFRACTIONr_mcangle_it0.4582980
X-RAY DIFFRACTIONr_scbond_it0.6093346
X-RAY DIFFRACTIONr_scangle_it0.9644.5319
LS refinement shellResolution: 2.96→3.032 Å / Num. reflection Rwork: 416 / Total num. of bins used: 20
Refinement TLS params.Method: refined / Origin x: 17.702 Å / Origin y: -31.6894 Å / Origin z: -6.6284 Å
111213212223313233
T0.0733 Å2-0.0128 Å2-0.0509 Å2-0.0641 Å2-0.0479 Å2--0.0961 Å2
L5.62 °2-1.7588 °21.7216 °2-2.3941 °2-2.4613 °2--3.6706 °2
S-0.0965 Å °-0.3893 Å °0.5775 Å °0.2285 Å °-0.0768 Å °-0.2431 Å °-0.297 Å °0.2149 Å °0.1733 Å °

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