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- PDB-1ekg: MATURE HUMAN FRATAXIN -

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Basic information

Entry
Database: PDB / ID: 1ekg
TitleMATURE HUMAN FRATAXIN
ComponentsFRATAXIN
KeywordsMETAL TRANSPORT / Freidreich's ataxia / iron transport / mitochondrial / disease
Function / homology
Function and homology information


regulation of ferrochelatase activity / [4Fe-4S] cluster assembly / proprioception / 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 iron-sulfur cluster assembly complex / positive regulation of aconitate hydratase activity ...regulation of ferrochelatase activity / [4Fe-4S] cluster assembly / proprioception / 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 iron-sulfur cluster assembly complex / positive regulation of aconitate hydratase activity / iron chaperone activity / negative regulation of organ growth / iron-sulfur cluster assembly complex / Mitochondrial protein import / [2Fe-2S] cluster assembly / adult walking behavior / oxidative phosphorylation / response to iron ion / embryo development ending in birth or egg hatching / iron-sulfur cluster assembly / heme biosynthetic process / muscle cell cellular homeostasis / negative regulation of multicellular organism growth / organ growth / positive regulation of catalytic activity / ferroxidase / negative regulation of release of cytochrome c from mitochondria / ferroxidase activity / protein autoprocessing / 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 / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily ...Frataxin/CyaY / Frataxin / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Frataxin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsDhe-Paganon, S. / Shigeta, R. / Chi, Y.I. / Ristow, M. / Shoelson, S.E.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of human frataxin.
Authors: Dhe-Paganon, S. / Shigeta, R. / Chi, Y.I. / Ristow, M. / Shoelson, S.E.
History
DepositionMar 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRATAXIN


Theoretical massNumber of molelcules
Total (without water)14,0451
Polymers14,0451
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.050, 45.220, 68.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FRATAXIN /


Mass: 14045.492 Da / Num. of mol.: 1 / Fragment: RESIDUES 88-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q16595
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.5 M ammonium sulfate, 0.1 sodium citrate, 2% sucrose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
25 mMTris1drop
30.3 M1dropNaCl
410 mMdithiothreitol1drop
52.5 Mammonium sulfate1reservoir
62 %sucrose1reservoir
7100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 12410 / Num. obs: 65773 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 23.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 27.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.288 / Num. unique all: 1090 / % possible all: 83.9
Reflection
*PLUS
Num. obs: 12410 / Num. measured all: 65773

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 629 -RANDOM
Rwork0.197 ---
all0.197 13254 --
obs0.197 12410 93.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 0 81 1021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_improper_angle_d0.71
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Num. reflection obs: 1090 / Rfactor obs: 0.291

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