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Yorodumi- PDB-1bzo: THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bzo | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY. | ||||||
Components | PROTEIN (SUPEROXIDE DISMUTASE) | ||||||
Keywords | OXIDOREDUCTASE / MONOMERIC CU / ZN SUPEROXIDE DISMUTASE / PROTEIN-SUBUNIT RECOGNITION / PROTEIN ELECTROSTATIC | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bordo, D. / Matak, D. / Djinovic-Carugo, K. / Rosano, C. / Pesce, A. / Bolognesi, M. / Stroppolo, M.E. / Falconi, M. / Battistoni, A. / Desideri, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase. Authors: Bordo, D. / Matak, D. / Djinovic-Carugo, K. / Rosano, C. / Pesce, A. / Bolognesi, M. / Stroppolo, M.E. / Falconi, M. / Battistoni, A. / Desideri, A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Novel Dimeric Interface and Electrostatic Recognition in Bacterial Cu,Zn Superoxide Dismutase Authors: Bourne, Y. / Redford, S.M. / Steinman, H.M. / Lepock, J.R. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bzo.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bzo.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 1bzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bzo_validation.pdf.gz | 406.7 KB | Display | wwPDB validaton report |
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Full document | 1bzo_full_validation.pdf.gz | 411.2 KB | Display | |
Data in XML | 1bzo_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1bzo_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bzo ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bzo | HTTPS FTP |
-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: 15813.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Cellular location: PERIPLASMIC SPACE / Production host: Escherichia coli (E. coli) / References: UniProt: P00446, superoxide dismutase | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | ChemComp-CU / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | ACTIVE SITE CATALYTIC ION COORDINATED TO HIS44, HIS46, HIS61 AND HIS118 ACTIVE SITE METAL ION ...ACTIVE SITE CATALYTIC ION COORDINATE | Sequence details | THE PROTEIN USED IS A TRUNCATED FORM, WITHOUT THE FIRST 22 RESIDUES | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 45.88 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, T=28C | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 28 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
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: X31 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→24.7 Å / Num. obs: 8469 / % possible obs: 96 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUS MODEL OF THE PROTEIN IN SPACE GROUP C2 NOT DEPOSITED IN PDB Resolution: 2.1→24.7 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
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Solvent computation | Bsol: 206 Å2 / ksol: 0.77 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.7 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_planar_d / Dev ideal: 0.01 |