+Open data
-Basic information
Entry | Database: PDB / ID: 4n3t | ||||||
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Title | Candida albicans Superoxide Dismutase 5 (SOD5), Cu(I) | ||||||
Components | Potential secreted Cu/Zn superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / antioxidant / oxidative burst / zinc loop / disulfide bond / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Galaleldeen, A. / Taylor, A.B. / Waninger-Saroni, J.J. / Holloway, S.P. / Hart, P.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Candida albicans SOD5 represents the prototype of an unprecedented class of Cu-only superoxide dismutases required for pathogen defense. Authors: Gleason, J.E. / Galaleldeen, A. / Peterson, R.L. / Taylor, A.B. / Holloway, S.P. / Waninger-Saroni, J. / Cormack, B.P. / 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 | 4n3t.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n3t.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 4n3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n3t_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 4n3t_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 4n3t_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4n3t_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/4n3t ftp://data.pdbj.org/pub/pdb/validation_reports/n3/4n3t | HTTPS FTP |
-Related structure data
Related structure data | 4n3uC 1azvS 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: 16896.715 Da / Num. of mol.: 1 / Fragment: UNP residues 27-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: CaO19.2060, CaO19.9607, SOD31, SOD5 / Plasmid: pAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5AD07 | ||||
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#2: Chemical | ChemComp-CU1 / | ||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: 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: 41.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.4 M ammonium sulfate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→102.2 Å / Num. obs: 28906 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 4138 / Rsym value: 0.569 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AZV Resolution: 1.4→31.72 Å / SU ML: 0.13 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.72 Å
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Refine LS restraints |
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LS refinement shell |
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