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- PDB-2bpi: Structure of Iron dependent superoxide dismutase from P. falciparum. -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bpi | ||||||
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Title | Structure of Iron dependent superoxide dismutase from P. falciparum. | ||||||
![]() | FE-SUPEROXIDE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / DISMUTASE / METAL-BINDING | ||||||
Function / homology | ![]() superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / response to oxidative stress / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boucher, I.W. / Brannigan, J. / Wilkinson, A.J. / Brzozowski, M. | ||||||
![]() | ![]() Title: The Crystal Structure of Superoxide Dismutase from Plasmodium Falciparum. Authors: Boucher, I.W. / Brzozowski, A.M. / Brannigan, J.A. / Schnick, C. / Smith, D.J. / Kyes, S.A. / Wilkinson, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iscS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99982, 0.01006, -0.01629), Vector: |
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Components
#1: Protein | Mass: 23831.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: PET 28C / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 7.5 / Details: 0.1M TRIS PH 7.5,38% PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 6, 2003 / Details: MIRRORS |
Radiation | Monochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→25 Å / Num. obs: 13247 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ISC Resolution: 2.52→59.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.172 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 6.219 / ESU R Free: 0.339 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→59.76 Å
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Refine LS restraints |
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