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- PDB-3oer: Crystal structure of trimeric frataxin from the yeast saccharomyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oer | ||||||
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Title | Crystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt | ||||||
![]() | Frataxin homolog, mitochondrial | ||||||
![]() | TRANSPORT PROTEIN / ALPHA/BETA SANDWICH / METALLOCHAPERONE / IRON-STORAGE | ||||||
Function / homology | ![]() Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ferroxidase activity ...Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ferroxidase activity / glutathione metabolic process / ferric iron binding / ferrous iron binding / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / iron ion transport / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soderberg, C.A.G. / Rajan, S. / Gakh, O. / Ta, C. / Isaya, G. / Al-Karadaghi, S. | ||||||
![]() | ![]() Title: Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering. Authors: Soderberg, C.A. / Shkumatov, A.V. / Rajan, S. / Gakh, O. / Svergun, D.I. / Isaya, G. / Al-Karadaghi, S. #1: ![]() Title: The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron Authors: Karlberg, T. / Schagerlof, U. / Gakh, O. / Park, S. / Ryde, U. / Lindahl, M. / Lleath, K. / Garman, E. / Isaya, G. / Al-Karadaghi, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
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Full document | ![]() | 430.1 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3oeqC ![]() 2fqlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13671.182 Da / Num. of mol.: 1 / Fragment: UNP residues 52-174 / Mutation: Y73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YFH1, YDL120W / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.43 Å3/Da / Density % sol: 77.33 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.7 M (NH4)2SO4, 0.2 M Li2SO4, 4 % -butyrolactone, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2008 |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.605 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 4752 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.38 |
Reflection shell | Resolution: 3.2→3.28 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FQL Resolution: 3.2→28.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 37.021 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.876 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→28.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.203→3.285 Å / Num. reflection Rwork: 334 / Total num. of bins used: 20 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 0.9051 Å / Origin y: -13.0806 Å / Origin z: -23.5434 Å
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