+Open data
-Basic information
Entry | Database: PDB / ID: 1t6u | ||||||
---|---|---|---|---|---|---|---|
Title | Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure | ||||||
Components | Superoxide dismutase [Ni] | ||||||
Keywords | OXIDOREDUCTASE / Nickel / 4-helix bundle / hexamer / superoxide dismutase / NiSOD / SOD / high resolution | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Barondeau, D.P. / Kassmann, C.J. / Bruns, C.K. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Nickel superoxide dismutase structure and mechanism. Authors: Barondeau, D.P. / Kassmann, C.J. / Bruns, C.K. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t6u.cif.gz | 640.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t6u.ent.gz | 525.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t6u_validation.pdf.gz | 497.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1t6u_full_validation.pdf.gz | 509.2 KB | Display | |
Data in XML | 1t6u_validation.xml.gz | 73.4 KB | Display | |
Data in CIF | 1t6u_validation.cif.gz | 106.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6u ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6u | HTTPS FTP |
-Related structure data
Related structure data | 1t6iSC 1t6qC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is hexameric |
-Components
#1: Protein | Mass: 13241.003 Da / Num. of mol.: 12 / Mutation: L85M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SODN, SOD1, SCO5254, 2SC7G11.16C / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P80735, superoxide dismutase #2: Chemical | ChemComp-NI / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPEG 5000, Hepes, methanol, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2003 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. all: 347604 / Num. obs: 347567 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 29263 / Rsym value: 0.365 / % possible all: 79.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T6I Resolution: 1.3→50 Å / Num. parameters: 119964 / Num. restraintsaints: 143755 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 17 / Occupancy sum hydrogen: 10899 / Occupancy sum non hydrogen: 13110 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell |
|