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- PDB-3t3t: 1.38 A structure of human frataxin variant Q148G -

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Basic information

Entry
Database: PDB / ID: 3t3t
Title1.38 A structure of human frataxin variant Q148G
ComponentsFrataxin, mitochondrial
KeywordsOXIDOREDUCTASE / Fe-S Cluster Biosynthesis / Human mitochondria
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 / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / iron-sulfur cluster assembly complex / Mitochondrial protein import / [2Fe-2S] cluster assembly / oxidative phosphorylation / 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 / positive regulation of catalytic activity / muscle cell cellular homeostasis / ferroxidase / negative regulation of release of cytochrome c from mitochondria / protein autoprocessing / ferroxidase activity / ferric iron binding / mitochondrion organization / 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: 1.38 Å
AuthorsBridwell-Rabb, J. / Winn, A.M. / Barondeau, D.P.
CitationJournal: Biochemistry / Year: 2011
Title: Structure-Function Analysis of Friedreich's Ataxia Mutants Reveals Determinants of Frataxin Binding and Activation of the Fe-S Assembly Complex.
Authors: Bridwell-Rabb, J. / Winn, A.M. / Barondeau, D.P.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Frataxin, mitochondrial
B: Frataxin, mitochondrial
C: Frataxin, mitochondrial
D: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8838
Polymers56,4984
Non-polymers3844
Water6,143341
1
A: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2212
Polymers14,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2212
Polymers14,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2212
Polymers14,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2212
Polymers14,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.410, 68.560, 89.970
Angle α, β, γ (deg.)90.00, 93.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14124.570 Da / Num. of mol.: 4 / Fragment: mature form (UNP residues 82-210) / Mutation: Q148G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXN, FRDA, X25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16595, ferroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0971 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0971 Å / Relative weight: 1
ReflectionResolution: 1.38→26.19 Å / Num. obs: 111516 / % possible obs: 96.7 %
Reflection shellResolution: 1.38→1.416 Å / % possible all: 94.24

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XFITdata reduction
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→26.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.979 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22656 5577 5 %RANDOM
Rwork0.19806 ---
all0.19947 ---
obs0.19947 111516 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.03 Å2
2--0.47 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.38→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 20 341 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0223892
X-RAY DIFFRACTIONr_angle_refined_deg2.51.9775285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66324.97167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46115658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6821510
X-RAY DIFFRACTIONr_chiral_restr0.1830.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212894
X-RAY DIFFRACTIONr_mcbond_it1.5771.52378
X-RAY DIFFRACTIONr_mcangle_it2.65423818
X-RAY DIFFRACTIONr_scbond_it4.03431514
X-RAY DIFFRACTIONr_scangle_it6.1694.51467
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 404 -
Rwork0.311 7622 -
obs-7622 94.24 %

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