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Yorodumi- PDB-6w1d: Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w1d | ||||||
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Title | Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2 | ||||||
Components |
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Keywords | TRANSFERASE / complex | ||||||
Function / homology | Function and homology information 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 iron-sulfur cluster 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 iron-sulfur cluster 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 / acyl binding / iron-sulfur cluster assembly / lipid biosynthetic process / lipid A biosynthetic process / acyl carrier activity / iron-sulfur cluster binding / phosphopantetheine binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / pyridoxal phosphate binding / Maturation of replicase proteins / intracellular iron ion homeostasis / molecular adaptor activity / nuclear body / mitochondrial matrix / response to xenobiotic stimulus / iron ion binding / centrosome / lipid binding / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å | ||||||
Authors | Boniecki, M.T. / Cygler, M. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w1d.cif.gz | 314.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w1d.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1d ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1d | HTTPS FTP |
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-Related structure data
Related structure data | 6uxeC 6wi2C 6wihC 7rtkC 5wlwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y697, cysteine desulfurase |
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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.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34 |
#3: Protein | Mass: 8514.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MJ81, UniProt: P0A6A8*PLUS |
#4: Protein | Mass: 15684.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1K1 |
-Non-polymers , 13 types, 464 molecules
#5: Chemical | ChemComp-PLP / | ||||||||||||||||||||||
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#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PEG / #9: Chemical | #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 | N |
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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: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M MES pH 6.0-6.5 22 % PEG 400 / PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.795→48.927 Å / Num. obs: 87545 / % possible obs: 99.94 % / Redundancy: 14.5 % / Biso Wilson estimate: 20.71 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.19 |
Reflection shell | Resolution: 1.795→1.859 Å / Redundancy: 14 % / Num. unique obs: 8566 / CC1/2: 0.835 / % possible all: 99.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WLW Resolution: 1.795→48.927 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.25 Å2 / Biso mean: 30.1661 Å2 / Biso min: 8.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.795→48.927 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % 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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