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- PDB-3s5e: Crystal structure of human frataxin variant W155R, one of the Fri... -

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Basic information

Entry
Database: PDB / ID: 3s5e
TitleCrystal structure of human frataxin variant W155R, one of the Friedreich's ataxia point mutations
ComponentsFrataxin, mitochondrial
KeywordsUNKNOWN FUNCTION / allosteric activator / mitochondrion / alpha beta 2-layer sandwich
Function / homology
Function and homology information


positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching ...positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching / Mitochondrial protein import / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / oxidative phosphorylation / response to iron ion / [2Fe-2S] cluster assembly / heme biosynthetic process / adult walking behavior / negative regulation of multicellular organism growth / organ growth / iron-sulfur cluster assembly / muscle cell cellular homeostasis / ferroxidase / negative regulation of release of cytochrome c from mitochondria / protein autoprocessing / ferroxidase activity / ferric iron binding / protein maturation / enzyme activator activity / iron ion transport / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / intracellular iron ion homeostasis / mitochondrial matrix / 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: 1.31 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)14,1912
Polymers14,1671
Non-polymers241
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.895, 49.215, 67.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14166.631 Da / Num. of mol.: 1 / Fragment: mature form (UNP residues 82-210) / Mutation: W155R
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG2000 MME, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Si(111), side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.31→39.69 Å / Num. obs: 31647 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Rsym value: 0.064 / Net I/σ(I): 22.2
Reflection shellResolution: 1.31→1.38 Å / Redundancy: 15 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.413 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
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: 1.31→39.69 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.431 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1593 5 %RANDOM
Rwork0.1508 ---
obs0.1531 31590 99.75 %-
all-31688 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 163.19 Å2 / Biso mean: 13.1792 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0 Å2
2--0.36 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.31→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 1 169 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022976
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.981323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16225.11643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32815170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181153
X-RAY DIFFRACTIONr_chiral_restr0.1340.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021727
X-RAY DIFFRACTIONr_mcbond_it2.6361.5600
X-RAY DIFFRACTIONr_mcangle_it3.7712965
X-RAY DIFFRACTIONr_scbond_it5.053376
X-RAY DIFFRACTIONr_scangle_it6.9044.5358
X-RAY DIFFRACTIONr_rigid_bond_restr2.7983976
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 123 -
Rwork0.165 2163 -
all-2286 -
obs--99.43 %

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