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Yorodumi- PDB-2goj: The crystal structure of the enzyme Fe-superoxide dismutase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2goj | ||||||
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Title | The crystal structure of the enzyme Fe-superoxide dismutase from Plasmodium falciparum | ||||||
Components | Fe-superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / BETA+ALPHA STRUCTURE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Navarro, M.V.A.S. / Garratt, R.C. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity Authors: Bachega, J.F. / Navarro, M.V. / Bleicher, L. / Bortoleto-Bugs, R.K. / Dive, D. / Hoffmann, P. / Viscogliosi, E. / Garratt, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2goj.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2goj.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 2goj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2goj_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 2goj_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 2goj_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2goj_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/2goj ftp://data.pdbj.org/pub/pdb/validation_reports/go/2goj | HTTPS FTP |
-Related structure data
Related structure data | 2gpcC 3esfC 1isaS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The assymetric unit contains a dimer, which represents the molecular assembly |
-Components
#1: Protein | Mass: 22630.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: HB3 / Gene: SOD / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 References: GenBank: 861077, UniProt: Q27740*PLUS, superoxide dismutase #2: Chemical | #3: 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: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25.5% PEG 4000 (w/v), 0.17 M Sodium Acetate, 0.085 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 10, 2002 |
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: 2→31.62 Å / Num. obs: 25131 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.098 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 73.3 |
-Processing
Software | Name: REFMAC / Version: 5.1.24 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISA Resolution: 2→31.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.711 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.191 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.498 Å2
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Refinement step | Cycle: LAST / Resolution: 2→31.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.108 Å / Total num. of bins used: 10 /
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