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- PDB-4ec2: Crystal structure of trimeric frataxin from the yeast Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 4ec2
TitleCrystal structure of trimeric frataxin from the yeast Saccharomyces cerevisiae, complexed with ferrous
ComponentsFrataxin homolog, mitochondrial
KeywordsTRANSPORT PROTEIN / alpha/beta sandwich / metallochaperone / iron-storage
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ferroxidase activity ...Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ferroxidase activity / glutathione metabolic process / ferric iron binding / ferrous iron binding / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / iron ion transport / intracellular iron ion homeostasis / response to oxidative stress / 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: 3.002 Å
AuthorsSoderberg, C.A.G. / Rajan, S. / Gakh, O. / Isaya, G. / Al-Karadaghi, S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization.
Authors: Soderberg, C.A. / Rajan, S. / Shkumatov, A.V. / Gakh, O. / Schaefer, S. / Ahlgren, E.C. / Svergun, D.I. / Isaya, G. / Al-Karadaghi, S.
#1: 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.G. / Shkumatov, A.V. / Rajan, S. / Gakh, O. / Svergun, D.I. / Isaya, G. / Al-karadaghi, S.
#2: 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. / Leath, K. / Garman, E. / Isaya, G. / Al-karadaghi, S.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frataxin homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7272
Polymers13,6711
Non-polymers561
Water00
1
A: Frataxin homolog, mitochondrial
hetero molecules

A: Frataxin homolog, mitochondrial
hetero molecules

A: Frataxin homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1816
Polymers41,0143
Non-polymers1683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area3890 Å2
ΔGint-42 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.570, 121.570, 121.570
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)
Strain: ATCC 204508 / S288c / Gene: YFH1, YDL120W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07540, ferroxidase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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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: 5.48 Å3/Da / Density % sol: 77.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.7 M (NH4)2SO4, 0.2 M Li2SO4, 4 % Gamma-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: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2008
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11254 / % possible obs: 96.9 % / Redundancy: 3.32 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.62
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.76 / Num. unique all: 791 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQL

2fql


Resolution: 3.002→24.815 Å / SU ML: 1.16 / σ(F): 1.29 / Phase error: 39.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3113 1097 9.76 %
Rwork0.2538 --
obs0.2597 11245 96.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.031 Å2 / ksol: 0.287 e/Å3
Refinement stepCycle: LAST / Resolution: 3.002→24.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 1 0 884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006903
X-RAY DIFFRACTIONf_angle_d1.2711233
X-RAY DIFFRACTIONf_dihedral_angle_d19.949339
X-RAY DIFFRACTIONf_chiral_restr0.088142
X-RAY DIFFRACTIONf_plane_restr0.008162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.002-3.13830.41351320.34871250X-RAY DIFFRACTION95
3.1383-3.30340.41491100.34411339X-RAY DIFFRACTION100
3.3034-3.50990.51021400.38051245X-RAY DIFFRACTION95
3.5099-3.780.49641400.34161215X-RAY DIFFRACTION95
3.78-4.15880.37521140.29131235X-RAY DIFFRACTION94
4.1588-4.75690.26541470.21281315X-RAY DIFFRACTION99
4.7569-5.97930.27611530.20081282X-RAY DIFFRACTION99
5.9793-24.81620.23151610.20861267X-RAY DIFFRACTION98

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