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Yorodumi- PDB-5wlw: Crystal Structure of the Human Mitochondrial Cysteine Desulfurase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wlw | ||||||
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Title | Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A. | ||||||
Components |
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Keywords | TRANSFERASE / Human mitochondrial cysteine desulfurse LYR Motif containing protein 4 Iron-Sulfur Cluster Scaffold Protein ISCU1 with Zn in the active site Acyl Carrier Protein 1 (E.coli) | ||||||
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 [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 / Maturation of TCA enzymes and regulation of TCA cycle / 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 | Homo sapiens (human) Escherichia coli O45:K1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.317 Å | ||||||
Authors | Boniecki, M.T. / Cygler, M. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Authors: Boniecki, M.T. / Freibert, S.A. / Muhlenhoff, U. / Lill, R. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wlw.cif.gz | 511 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wlw.ent.gz | 418.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wlw_validation.pdf.gz | 786.8 KB | Display | wwPDB validaton report |
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Full document | 5wlw_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 5wlw_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 5wlw_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wlw ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wlw | HTTPS FTP |
-Related structure data
Related structure data | 5wgbC 5wkpC 2faeS 3lmvS 3lvlS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 45081.578 Da / Num. of mol.: 2 / Fragment: UNP residues 56-457 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 #2: Protein | Mass: 10763.483 Da / Num. of mol.: 2 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria) Strain: S88 / ExPEC / Gene: acpP, ECS88_1108 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MJ81 #4: Protein | Mass: 16337.819 Da / Num. of mol.: 2 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 |
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-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | |
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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: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 7.0 15 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→48.85 Å / Num. obs: 27282 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.997 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 3.3→3.52 Å / Mean I/σ(I) obs: 2.73 / CC1/2: 0.87 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LMV, 3LVL, 2FAE Resolution: 3.317→48.764 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.317→48.764 Å
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Refine LS restraints |
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LS refinement shell |
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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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