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Yorodumi- PDB-1xtl: Crystal structure of P104H mutant of SOD-like protein from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xtl | ||||||
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Title | Crystal structure of P104H mutant of 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: 2 Å | ||||||
Authors | Calderone, V. / Mangani, S. / Banci, L. / Benvenuti, M. / Bertini, I. / Viezzoli, M.S. / Fantoni, A. | ||||||
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 | 1xtl.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xtl.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xtl_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 1xtl_full_validation.pdf.gz | 494.7 KB | Display | |
Data in XML | 1xtl_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 1xtl_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xtl ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xtl | HTTPS FTP |
-Related structure data
Related structure data | 1xtmC 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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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: 18779.824 Da / Num. of mol.: 4 / Mutation: 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 | ChemComp-CU / #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: 2.4 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na Acetate, 20% PEG4000, 0.1M Ammonium Sulphate, 10mM 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: 1.3711 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 22, 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: 1.3711 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.958 Å / Num. all: 41966 / Num. obs: 41966 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 28.733 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5985 / Rsym value: 0.244 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S4I Resolution: 2→38.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.115 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.241 / ESU R Free: 0.219 / 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: 26.755 Å2
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Refine analyze | Luzzati sigma a obs: 0.168 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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