+Open data
-Basic information
Entry | Database: PDB / ID: 5kbk | ||||||
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Title | Candida Albicans Superoxide Dismutase 5 (SOD5), E110A Mutant | ||||||
Components | Cell surface Cu-only superoxide dismutase 5 | ||||||
Keywords | OXIDOREDUCTASE / Antioxidant / Oxidative burst / Zinc loop / Extracellular | ||||||
Function / homology | Function and homology information symbiont defense to host-produced reactive oxygen species / cellular response to superoxide / hyphal cell wall / fungal-type cell wall / evasion of host immune response / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / side of membrane / removal of superoxide radicals ...symbiont defense to host-produced reactive oxygen species / cellular response to superoxide / hyphal cell wall / fungal-type cell wall / evasion of host immune response / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / side of membrane / removal of superoxide radicals / cellular response to oxidative stress / copper ion binding / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.411 Å | ||||||
Authors | Galaleldeen, A. / Peterson, R.L. / Villarreal, J. / Taylor, A.B. / Hart, P.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: The Phylogeny and Active Site Design of Eukaryotic Copper-only Superoxide Dismutases. Authors: Peterson, R.L. / Galaleldeen, A. / Villarreal, J. / Taylor, A.B. / Cabelli, D.E. / Hart, P.J. / Culotta, V.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kbk.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kbk.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kbk ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kbk | HTTPS FTP |
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-Related structure data
Related structure data | 5kblC 5kbmC 4n3tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16838.680 Da / Num. of mol.: 1 / Fragment: residues 27-181 / Mutation: E110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: SOD5, PGA3, SOD31, CaO19.2060, CaO19.9607 / Plasmid: pAG8H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5AD07, superoxide dismutase | ||
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#2: Chemical | ChemComp-CU1 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES monohydrate pH 6.0, 2.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→40.61 Å / Num. obs: 25403 / % possible obs: 90.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.5 Å2 / CC1/2: 0.999 / Rsym value: 0.041 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.41→1.49 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 13 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N3T Resolution: 1.411→28.471 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 16.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.411→28.471 Å
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Refine LS restraints |
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LS refinement shell |
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