+Open data
-Basic information
Entry | Database: PDB / ID: 3ak3 | ||||||
---|---|---|---|---|---|---|---|
Title | Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form | ||||||
Components | Superoxide dismutase [Mn/Fe] | ||||||
Keywords | OXIDOREDUCTASE / superoxide dismutase / cambialistic | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å | ||||||
Authors | Nakamura, T. / Uegaki, K. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability Authors: Nakamura, T. / Torikai, K. / Uegaki, K. / Morita, J. / Machida, K. / Suzuki, A. / Kawata, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ak3.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ak3.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ak3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3ak3 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3ak3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ak1SC 3ak2C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24609.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE0741 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9Y8H8, superoxide dismutase #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 10% PEG 6000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 124631 / Num. obs: 119558 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.324 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.6 / Num. unique all: 11055 / % possible all: 88.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3AK1 Resolution: 1.48→49.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.883 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.463 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→49.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.48→1.519 Å / Total num. of bins used: 20
|