+Open data
-Basic information
Entry | Database: PDB / ID: 1ibh | ||||||
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Title | X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT M41I | ||||||
Components | CU,ZN SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / prokaryotic superoxide dismutase / subunit interaction | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Photobacterium leiognathi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Stroppolo, M.E. / Pesce, A. / D'Orazio, M. / O'Neill, P. / Bordo, D. / Rosano, C. / Milani, M. / Battistoni, A. / Bolognesi, M. / Desideri, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase. Authors: Stroppolo, M.E. / Pesce, A. / D'Orazio, M. / O'Neill, P. / Bordo, D. / Rosano, C. / Milani, M. / Battistoni, A. / Bolognesi, M. / Desideri, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ibh.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ibh.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ibh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ibh_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 1ibh_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 1ibh_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1ibh_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/1ibh ftp://data.pdbj.org/pub/pdb/validation_reports/ib/1ibh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15795.815 Da / Num. of mol.: 1 / Mutation: M41I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00446, superoxide dismutase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CU / |
#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: 2.21 Å3/Da / Density % sol: 44.35 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 1999 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→18 Å / Num. all: 9449 / Num. obs: 9449 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 26 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 106644 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: P.leiognathi Cu,Zn SOD wild type Resolution: 2→18 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→18 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.229 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 |