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- PDB-3s5d: Crystal structure of human frataxin variant W155A -

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Basic information

Entry
Database: PDB / ID: 3s5d
TitleCrystal structure of human frataxin variant W155A
ComponentsFrataxin, mitochondrial
KeywordsUNKNOWN FUNCTION / allosteric activator / mitochondrion / alpha beta 2-layer sandwich
Function / homology
Function and homology information


regulation of ferrochelatase activity / proprioception / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity ...regulation of ferrochelatase activity / proprioception / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity / iron chaperone activity / negative regulation of organ growth / iron-sulfur cluster assembly complex / Mitochondrial protein import / oxidative phosphorylation / [2Fe-2S] cluster assembly / adult walking behavior / response to iron ion / embryo development ending in birth or egg hatching / iron-sulfur cluster assembly / heme biosynthetic process / negative regulation of multicellular organism growth / organ growth / muscle cell cellular homeostasis / positive regulation of catalytic activity / ferroxidase / negative regulation of release of cytochrome c from mitochondria / protein autoprocessing / ferroxidase activity / mitochondrion organization / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / iron ion transport / positive regulation of cell growth / intracellular iron ion homeostasis / mitochondrial matrix / positive regulation of cell population proliferation / negative regulation of apoptotic process / mitochondrion / cytosol
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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTsai, C.-L. / Bridwell-Rabb, J. / Barondeau, D.P.
CitationJournal: Biochemistry / Year: 2011
Title: Friedreich's Ataxia Variants I154F and W155R Diminish Frataxin-Based Activation of the Iron-Sulfur Cluster Assembly Complex.
Authors: Tsai, C.L. / Bridwell-Rabb, J. / Barondeau, D.P.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1772
Polymers14,0811
Non-polymers961
Water1,838102
1
A: Frataxin, mitochondrial
hetero molecules

A: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3534
Polymers28,1612
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1830 Å2
ΔGint-39 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 32.260, 44.810
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Frataxin, mitochondrial / Friedreich ataxia protein / Fxn


Mass: 14080.516 Da / Num. of mol.: 1 / Fragment: mature form (UNP residues 82-210) / Mutation: W155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRDA, FXN, X25 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16595, ferroxidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationMonochromator: Si(111), Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.5→44.8 Å / Num. obs: 20101 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.138 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.483 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EKG

1ekg


Resolution: 1.5→44.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.939 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1022 5.1 %RANDOM
Rwork0.1686 ---
obs0.1698 20074 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.33 Å2 / Biso mean: 10.0966 Å2 / Biso min: 2.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.03 Å2
2--0.31 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 5 102 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022987
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.9851342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14725.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.936152
X-RAY DIFFRACTIONr_chiral_restr0.1650.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021730
X-RAY DIFFRACTIONr_mcbond_it1.6951.5605
X-RAY DIFFRACTIONr_mcangle_it2.5072977
X-RAY DIFFRACTIONr_scbond_it3.3663382
X-RAY DIFFRACTIONr_scangle_it5.2414.5365
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 65 -
Rwork0.174 1396 -
all-1461 -
obs--97.73 %

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