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Yorodumi- PDB-3u9j: Crystal structure of oxidized human FBXL5 hemerythrin like domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u9j | ||||||
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Title | Crystal structure of oxidized human FBXL5 hemerythrin like domain | ||||||
Components | F-box/LRR-repeat protein 5 | ||||||
Keywords | PROTEIN BINDING / FBOX / LRR / Ubiquitin ligase E3 / iron sensor | ||||||
Function / homology | Function and homology information SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation ...SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / intracellular iron ion homeostasis / protein ubiquitination / iron ion binding / perinuclear region of cytoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.603 Å | ||||||
Authors | Li, P. | ||||||
Citation | Journal: Chembiochem / Year: 2012 Title: The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5. Authors: Shu, C. / Sung, M.W. / Stewart, M.D. / Igumenova, T.I. / Tan, X. / Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u9j.cif.gz | 150.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u9j.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 3u9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u9j ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19558.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL5, FBL4, FBL5, FLR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKA1 #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2011 |
Radiation | Monochromator: Si-Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32 Å / Num. all: 44592 / Num. obs: 44325 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.603→31.881 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 27.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.531 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.603→31.881 Å
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Refine LS restraints |
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LS refinement shell |
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