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- PDB-3oer: Crystal structure of trimeric frataxin from the yeast saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 3oer
TitleCrystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt
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: 3.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7302
Polymers13,6711
Non-polymers591
Water28816
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)41,1906
Polymers41,0143
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3580 Å2
ΔGint-49 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.200, 121.200, 121.200
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
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 5.43 Å3/Da / Density % sol: 77.33 %
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: I911-3 / Wavelength: 1.605 Å
DetectorType: MARMOSAIC 225 mm CCD / 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: 1.605 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 4752 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.38
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0044refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQL

2fql


Resolution: 3.2→28.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 37.021 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 484 9.7 %RANDOM
Rwork0.20417 ---
all0.20883 4530 --
obs0.20883 4530 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.876 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 1 16 893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022896
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9891225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6475111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.72226.58541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.91515150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.477152
X-RAY DIFFRACTIONr_chiral_restr0.1380.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022680
X-RAY DIFFRACTIONr_mcbond_it0.4851.5563
X-RAY DIFFRACTIONr_mcangle_it0.9412915
X-RAY DIFFRACTIONr_scbond_it1.2333333
X-RAY DIFFRACTIONr_scangle_it2.254.5310
LS refinement shellResolution: 3.203→3.285 Å / Num. reflection Rwork: 334 / Total num. of bins used: 20
Refinement TLS params.Method: refined / Origin x: 0.9051 Å / Origin y: -13.0806 Å / Origin z: -23.5434 Å
111213212223313233
T0.0899 Å2-0.0339 Å20.0658 Å2-0.2672 Å20.0932 Å2--0.2689 Å2
L4.3208 °2-4.054 °23.6804 °2-7.29 °2-2.674 °2--4.5739 °2
S0.1218 Å °0.6326 Å °0.5044 Å °-0.4256 Å °-0.186 Å °-0.8856 Å °0.0684 Å °0.7541 Å °0.0643 Å °

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