+Open data
-Basic information
Entry | Database: PDB / ID: 1eso | ||||||
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Title | MONOMERIC CU,ZN SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI | ||||||
Components | CU, ZN SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / CU / ZN SUPEROXIDE DISMUTASE / MONOMERIC SUPEROXIDE DISMUTASE / COPPER ENZYMES / ENZYME EVOLUTION / X-RAY CRYSTAL STRUCTURE | ||||||
Function / homology | Function and homology information superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pesce, A. / Capasso, C. / Battistoni, A. / Folcarelli, S. / Rotilio, G. / Desideri, A. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Unique structural features of the monomeric Cu,Zn superoxide dismutase from Escherichia coli, revealed by X-ray crystallography. Authors: Pesce, A. / Capasso, C. / Battistoni, A. / Folcarelli, S. / Rotilio, G. / Desideri, A. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eso.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eso.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 1eso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1eso ftp://data.pdbj.org/pub/pdb/validation_reports/es/1eso | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15760.583 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BMH 71-18 / Cellular location: PERIPLASM / Gene: SODC / Production host: Escherichia coli (E. coli) References: UniProt: P53635, UniProt: P0AGD1*PLUS, 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: 2.1 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 40 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 7, 1996 / Details: PINHOLE COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→26.3 Å / Num. obs: 9044 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.07 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 28077 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY SIRAS IN THE DEPOSITORS' LAB Resolution: 2→26 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT: ENGH-HUBER
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Solvent computation | Solvent model: TNT / Bsol: 103.3 Å2 / ksol: 0.76 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→26 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5B / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 9057 / Num. reflection obs: 8624 / Rfactor all: 0.168 / Rfactor Rfree: 0.263 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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