+Open data
-Basic information
Entry | Database: PDB / ID: 3lvl | ||||||
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Title | Crystal Structure of E.coli IscS-IscU complex | ||||||
Components |
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Keywords | TRANSFERASE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Fe-S cluster assembly / sulfur transfer | ||||||
Function / homology | Function and homology information cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / iron ion binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shi, R. / Proteau, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Plos Biol. / Year: 2010 Title: Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions. Authors: Shi, R. / Proteau, A. / Villarroya, M. / Moukadiri, I. / Zhang, L. / Trempe, J.F. / Matte, A. / Armengod, M.E. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lvl.cif.gz | 210.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lvl.ent.gz | 167.6 KB | Display | PDB format |
PDBx/mmJSON format | 3lvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lvl_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 3lvl_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 3lvl_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3lvl_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/3lvl ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lvl | HTTPS FTP |
-Related structure data
Related structure data | 3lvjC 3lvkC 3lvmC 1p3wS 2z7eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47326.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: iscS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6B9, cysteine desulfurase |
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#2: Protein | Mass: 13878.507 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: iscU / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACD6 |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 16% PEG 8000, 0.2M Sodium Nitrate, 4% Glycerol, 0.1M Bicine pH 9.0, vapor diffusion, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 11488 / % possible obs: 83.4 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.093 / Χ2: 0.997 / Net I/σ(I): 12.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P3W and 2Z7E Resolution: 3→44.489 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / 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 / Bsol: 24.069 Å2 / ksol: 0.325 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.84 Å2 / Biso mean: 65.786 Å2 / Biso min: 45.22 Å2
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Refinement step | Cycle: LAST / Resolution: 3→44.489 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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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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