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Yorodumi- PDB-2cx3: Crystal structure of a bacterioferritin comigratory protein perox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cx3 | ||||||
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Title | Crystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-1 crystal) | ||||||
Components | bacterioferritin comigratory protein | ||||||
Keywords | OXIDOREDUCTASE / antioxidant enzyme / reactive oxygen species / thioredoxin fold / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å | ||||||
Authors | Mizohata, E. / Murayama, K. / Idaka, M. / Tatsuguchi, A. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-1 crystal) Authors: Mizohata, E. / Murayama, K. / Idaka, M. / Tatsuguchi, A. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cx3.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cx3.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cx3 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cx3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18835.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE2125 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: GenBank: 14601861, UniProt: Q9YA14*PLUS, peroxiredoxin #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: 3.27 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, 2-propanol, Tris, sodium chloride, dithiothreitol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96400, 0.97909, 0.97942 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 1, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.64→50 Å / Num. obs: 54115 / Biso Wilson estimate: 38 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.64→47.33 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: The crystal form is twinned by the operator k, h, -l, twinning fraction 0.5
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Displacement parameters | Biso mean: 64.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.64→47.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.73 Å / Total num. of bins used: 10
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