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- PDB-3s5f: Crystal structure of human frataxin variant W155F -

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Basic information

Entry
Database: PDB / ID: 3s5f
TitleCrystal structure of human frataxin variant W155F
ComponentsFrataxin, mitochondrial
KeywordsUNKNOWN FUNCTION / allosteric activator / mitochondrion / alpha beta 2-layer sandwich
Function / homology
Function and homology information


regulation of ferrochelatase activity / proprioception / iron incorporation into metallo-sulfur cluster / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / [4Fe-4S] cluster assembly / positive regulation of aconitate hydratase activity / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity ...regulation of ferrochelatase activity / proprioception / iron incorporation into metallo-sulfur cluster / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / [4Fe-4S] cluster assembly / positive regulation of aconitate hydratase activity / 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 [2Fe-2S] assembly complex / Mitochondrial protein import / iron-sulfur cluster assembly complex / positive regulation of catalytic activity / oxidative phosphorylation / response to iron ion / embryo development ending in birth or egg hatching / [2Fe-2S] cluster assembly / adult walking behavior / heme biosynthetic process / negative regulation of multicellular organism growth / organ growth / muscle cell cellular homeostasis / iron-sulfur cluster assembly / ferroxidase / negative regulation of release of cytochrome c from mitochondria / ferroxidase activity / protein autoprocessing / 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: 1.5 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,3624
Polymers28,3132
Non-polymers492
Water2,486138
1
A: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1812
Polymers14,1571
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1812
Polymers14,1571
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.680, 53.120, 48.480
Angle α, β, γ (deg.)90.000, 112.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14156.611 Da / Num. of mol.: 2 / Fragment: mature form (UNP residues 82-210) / Mutation: W155F
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, 30% PEG4000, pH 8.5, 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 7, 2011
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: 1.5→44.854 Å / Num. obs: 35399 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.072 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.884 / % possible all: 97.2

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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: 1.5→44.85 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 3.556 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1769 5 %RANDOM
Rwork0.1635 ---
obs0.166 35368 97.26 %-
all-36363 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.54 Å2 / Biso mean: 22.3357 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.19 Å2
2--0.27 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 2 138 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221991
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9762704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3325.39389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.896154
X-RAY DIFFRACTIONr_chiral_restr0.2030.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211488
X-RAY DIFFRACTIONr_mcbond_it2.4211.51221
X-RAY DIFFRACTIONr_mcangle_it3.66521971
X-RAY DIFFRACTIONr_scbond_it5.4633770
X-RAY DIFFRACTIONr_scangle_it7.8244.5733
X-RAY DIFFRACTIONr_rigid_bond_restr2.69331991
LS refinement shellResolution: 1.495→1.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 133 -
Rwork0.274 2464 -
all-2597 -
obs--96.54 %

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