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- PDB-7rtk: Structure of the (NIAU)2 complex with N-terminal mutation of ISCU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rtk | ||||||
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Title | Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution | ||||||
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![]() | TRANSFERASE / complex | ||||||
Function / homology | ![]() negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone ...negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / lipid A biosynthetic process / iron-sulfur cluster binding / acyl binding / acyl carrier activity / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / Maturation of replicase proteins / intracellular iron ion homeostasis / molecular adaptor activity / nuclear body / mitochondrial matrix / iron ion binding / centrosome / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boniecki, M.T. / Cygler, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis Authors: Freibert, S.A. / Boniecki, M.T. / Shulz, V. / Wilbrecht, C. / Krapoth, N. / Muhlenhoff, U. / Stehling, O. / Cygler, M. / Lill, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298 KB | Display | ![]() |
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PDB format | ![]() | 235.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uxeSC ![]() 6w1dC ![]() 6wi2C ![]() 6wihC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 45081.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10763.483 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 8514.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 15636.033 Da / Num. of mol.: 1 / Mutation: Y35D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 13 types, 260 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P15.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDT.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P15.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDT.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PLP / | ||||||||||||||||||||||
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#6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-PEG / #10: Chemical | ChemComp-P15 / | #11: Chemical | ChemComp-DTT / | #12: Chemical | #13: Chemical | ChemComp-EDT / {[-( | #14: Chemical | ChemComp-8Q1 / | #15: Chemical | ChemComp-MES / | #16: Chemical | ChemComp-1PE / | #17: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES pH 5.5 22.5 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→49 Å / Num. obs: 33254 / % possible obs: 100 % / Redundancy: 12.924 % / Biso Wilson estimate: 44.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.157 / Χ2: 0.969 / Net I/σ(I): 14.26 / Num. measured all: 429761 / Scaling rejects: 57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UXE Resolution: 2.5→49 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.97 Å2 / Biso mean: 49.2438 Å2 / Biso min: 19.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→49 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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