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Yorodumi- PDB-1z9n: X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z9n | ||||||
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Title | X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / CU-ZN SOD / SOD / HAEM | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Haemophilus ducreyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Djinovic Carugo, K. / Toeroe, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi. Authors: Toro, I. / Petrutz, C. / Pacello, F. / D'Orazio, M. / Battistoni, A. / Djinovic-Carugo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z9n.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z9n.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9n ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9n | HTTPS FTP |
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-Related structure data
Related structure data | 1z9pC 2apsS 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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2 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 19120.766 Da / Num. of mol.: 4 / Fragment: MATURE PROTEIN WITH HAEM BOUND Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: sodC / Production host: Escherichia coli (E. coli) / References: UniProt: Q59452, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 8000, sodium cacodylate, sodium acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 12, 2001 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.5 Å / Num. all: 88269 / Num. obs: 88269 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.284 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2.99 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.53 / Num. unique all: 13302 / Rsym value: 0.278 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2APS Resolution: 1.5→19.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.838 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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