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Yorodumi- PDB-1xtm: Crystal structure of the double mutant Y88H-P104H of a SOD-like p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xtm | ||||||
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Title | Crystal structure of the double mutant Y88H-P104H of a SOD-like protein from Bacillus subtilis. | ||||||
Components | Hypothetical superoxide dismutase-like protein yojM | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SOD / Cu-Zn SOD / SOD-like / superoxide dismutase mutants | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Calderone, V. / Mangani, S. / Banci, L. / Benvenuti, M. / Bertini, I. / Fantoni, A. / Viezzoli, M.S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis. Authors: Banci, L. / Benvenuti, M. / Bertini, I. / Cabelli, D.E. / Calderone, V. / Fantoni, A. / Mangani, S. / Migliardi, M. / Viezzoli, M.S. #1: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xtm.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xtm.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xtm_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 1xtm_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 1xtm_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1xtm_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xtm ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xtm | HTTPS FTP |
-Related structure data
Related structure data | 1xtlC 1s4iS 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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2 |
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3 |
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Unit cell |
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Details | The protein is a monomer in vivo but there are two molecules. |
-Components
#1: Protein | Mass: 18754.797 Da / Num. of mol.: 2 / Mutation: Y67H, P83H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP1 / References: UniProt: O31851 #2: Chemical | #3: Chemical | ChemComp-ZN / #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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na Acetate, 30% PEG4000, 0.2M Ammonium Sulphate, 1mM ZnCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.2768 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2004 / Details: Double crystal focussing mono chromator |
Radiation | Monochromator: Double crystal focussing mono chromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2768 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.8 Å / Num. all: 43173 / Num. obs: 43173 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 21.907 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6245 / Rsym value: 0.478 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S4I Resolution: 1.6→25.6 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.43 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.11 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.866 Å2
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Refine analyze | Luzzati sigma a obs: 0.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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