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Yorodumi- PDB-6akz: Crystal structure of GlcNAc Inducible Gene 2, GIG2 (DUF1479) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6akz | ||||||
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Title | Crystal structure of GlcNAc Inducible Gene 2, GIG2 (DUF1479) from Candida albicans | ||||||
Components | GlcNAc Inducible Gene 2, GIG2 | ||||||
Keywords | OXIDOREDUCTASE / GIG / candida | ||||||
Function / homology | Gig2-like / Gig2-like / Isopenicillin N synthase-like superfamily / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Gautam, G. / Rani, P. / Dutta, A. / Gourinath, S. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Crystal structure of Gig2 protein from Candida albicans provides a structural insight into DUF1479 family oxygenases. Authors: Rani, P. / Gautam, G. / Anwar, T. / Gourinath, S. / Datta, A. #1: Journal: Journal of Proteins & Proteomics / Year: 2017 Title: CLONING, EXPRESSION, PURIFICATION AND CRYSTALLIZATION OF A NOVEL GLCNAC METABOLIC PROTEIN, GIG2 (DUF1479) FROM PATHOGENIC FUNGUS CANDIDA ALBICANS Authors: Rani, P. / Gautam, G. / Rao, H.K. / Ghosh, S. / Gourinath, S. / Dhar, S.K. / Dutta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6akz.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6akz.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 6akz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akz ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akz | HTTPS FTP |
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-Related structure data
Related structure data | 2csgS 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: 54892.746 Da / Num. of mol.: 1 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: orf19.4783, CAALFM_C109240CA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8PEJ2 |
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#2: Chemical | ChemComp-FE / |
#3: 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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 6000, 0.1M Tris pH 8.0, 0.1M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→72.09 Å / Num. obs: 52149 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.69→1.75 Å / Rmerge(I) obs: 1.001 / Num. unique obs: 4894 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CSG Resolution: 1.69→72.09 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.766 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.728 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→72.09 Å
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Refine LS restraints |
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