+Open data
-Basic information
Entry | Database: PDB / ID: 1s4i | ||||||
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Title | Crystal structure of a SOD-like protein from Bacillus subtilis | ||||||
Components | superoxide dismutase-like protein yojM | ||||||
Keywords | OXIDOREDUCTASE / SOD / Cu-Zn SOD / SOD-like / superoxide dismutase | ||||||
Function / homology | Function and homology information superoxide dismutase activity / removal of superoxide radicals / copper ion binding / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Banci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal. Authors: Banci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THE BIOLOGICAL UNIT APPEARS TO BE A MONOMER. | ||||||
Remark 999 | SEQUENCE THE AUTHORS STATE THE SEQUENCE IN THE SEQRES CORRESPONDS TO THE ONE CLONED BUT THEY STATE ...SEQUENCE THE AUTHORS STATE THE SEQUENCE IN THE SEQRES CORRESPONDS TO THE ONE CLONED BUT THEY STATE IT IS LIKELY THAT SOME RESIDUES AT THE N-TERMINUS ARE CLEAVED OFF DURING CRYSTALLISATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s4i.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s4i.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s4i_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
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Full document | 1s4i_full_validation.pdf.gz | 504.3 KB | Display | |
Data in XML | 1s4i_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 1s4i_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4i ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The protein is a monomer in vivo but there are four molecules in the asymmetric unit. |
-Components
#1: Protein | Mass: 18738.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YOJM, BSU19400 / Production host: Escherichia coli (E. coli) / References: UniProt: O31851, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: 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: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: TRIS, Ammonium sulphate, PEG4000, LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.281 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2003 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.281 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.07 Å / Num. all: 49677 / Num. obs: 49677 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 29.17 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3958 / Rsym value: 0.23 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→37.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.27 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.868 Å2
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Refine analyze | Luzzati sigma a obs: 0.125 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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