+Open data
-Basic information
Entry | Database: PDB / ID: 1t6i | ||||||
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Title | Nickel Superoxide Dismutase (NiSOD) Apo Structure | ||||||
Components | Superoxide dismutase [Ni] | ||||||
Keywords | OXIDOREDUCTASE / Nickel / 4-helix bundle / hexamer / superoxide dismutase / NiSOD / SOD / apo | ||||||
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 / MAD / Resolution: 2.81 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6i.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6i.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1t6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t6i_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 1t6i_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 1t6i_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1t6i_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6i ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operation -x,y,-z+1/2 |
-Components
#1: Protein | Mass: 13512.885 Da / Num. of mol.: 3 / Mutation: L85M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SODN, SOD1, SCO5254, 2SC7G11.16C / Plasmid: PET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P80735, superoxide dismutase #2: 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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPEG 2000, Hepes, methanol, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.911656, 0.97912, 0.979311 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 11, 2000 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→20 Å / Num. all: 9300 / Num. obs: 9300 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 63 Å2 / Rsym value: 0.059 / Net I/σ(I): 22.4 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4.3 / Num. unique all: 912 / Rsym value: 0.267 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.81→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 309608.65 / Data cutoff high rms absF: 309608.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.289707 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.81→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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