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Open data
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Basic information
Entry | Database: PDB / ID: 1ib5 | ||||||
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Title | X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83Y | ||||||
![]() | CU,ZN SUPEROXIDE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / prokaryotic superoxide dismutase / subunit interaction | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stroppolo, M.E. / Pesce, A. / D'Orazio, M. / O'Neill, P. / Bordo, D. / Rosano, C. / Milani, M. / Battistoni, A. / Bolognesi, M. / Desideri, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.7 KB | Display | ![]() |
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PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.4 KB | Display | ![]() |
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Full document | ![]() | 418.7 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15790.817 Da / Num. of mol.: 1 / Mutation: W83Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % | ||||||||||||||||||||||||||||||
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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: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. all: 5289 / Num. obs: 5289 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.23 / Rsym value: 0.23 / Net I/σ(I): 5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 33184 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: P.leiognathi Cu,Zn SOD wild type Resolution: 2.45→20 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28 Å2 |