[English] 日本語
Yorodumi- PDB-1z9p: X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z9p | ||||||
---|---|---|---|---|---|---|---|
Title | X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / CU-ZN SOD / SOD / METALLOENZYMES | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1z9p.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1z9p.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 1z9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9p ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9p | HTTPS FTP |
---|
-Related structure data
Related structure data | 1z9nSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 16514.764 Da / Num. of mol.: 2 / Fragment: residues 45-199 Source method: isolated from a genetically manipulated source Details: mature protein without bound HAEM / Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: sodC / Plasmid: pHEN-1 / Production host: Escherichia coli (E. coli) / Strain (production host): 71/18 / References: UniProt: Q59452, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium cytrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 10, 2001 / Details: mirrors |
Radiation | Monochromator: double-crystal monochromator in non-dispersive configuration with two interchangeable pairs of crystals - Si(111) and Si(220) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 46454 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.93 % / Biso Wilson estimate: 23.455 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17.99 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 6.62 / Num. unique all: 6883 / Rsym value: 0.178 / % possible all: 91.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z9N Resolution: 1.5→19.32 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.442 / SU ML: 0.053 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.471 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
|