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Yorodumi- PDB-1gn2: S123C mutant of the iron-superoxide dismutase from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gn2 | ||||||
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Title | S123C mutant of the iron-superoxide dismutase from Mycobacterium tuberculosis. | ||||||
Components | SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / IRON | ||||||
Function / homology | Function and homology information detoxification / Tolerance of reactive oxygen produced by macrophages / superoxide dismutase / superoxide dismutase activity / manganese ion binding / response to oxidative stress / periplasmic space / iron ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Bunting, K.A. / Cooper, J.B. / Tickle, I.J. / Young, D.B. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2002 Title: Engineering of an Intersubunit Disulfide Bridge in the Iron-Superoxide Dismutase of Mycobacterium Tuberculosis. Authors: Bunting, K.A. / Cooper, J.B. / Tickle, I.J. / Young, D.B. #1: Journal: Eur.J.Biochem. / Year: 1998 Title: Engineering a Change in Metal-Ion Specificity of the Iron-Dependent Superoxide Dismutase from Mycobacterium Tuberculosis-- X-Ray Structure Analysis of Site-Directed Mutants Authors: Bunting, K. / Cooper, J.B. / Badasso, M.O. / Tickle, I.J. / Newton, M. / Wood, S.P. / Zhang, Y. / Young, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gn2.cif.gz | 271.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gn2.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/1gn2 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/1gn2 | HTTPS FTP |
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-Related structure data
Related structure data | 1idsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23076.926 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: MYCOBACTERIUM VACCAE (bacteria) References: UniProt: P17670, UniProt: P9WGE7*PLUS, superoxide dismutase #2: Chemical | ChemComp-FE / Compound details | ENGINEERED | |
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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: 2.26 Å3/Da / Density % sol: 39.7 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 100MM TRIS-HCL PH 7.0, 25% PEG 6000, PROTEIN CONCENTRATION = 3 MG/ML. | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→24 Å / Num. obs: 15208 / % possible obs: 67.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / % possible all: 67.7 |
Reflection | *PLUS Lowest resolution: 24 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IDS Resolution: 3.4→21 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: INDIVIDUAL B-FACTORS NO REFINED.
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Refinement step | Cycle: LAST / Resolution: 3.4→21 Å
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Refine LS restraints |
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Software | *PLUS Name: CCP4 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 21 Å / Rfactor obs: 0.249 / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |