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Open data
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Basic information
Entry | Database: PDB / ID: 7o8d | ||||||
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Title | diFe-sulerythrin oxidised by H2O2 | ||||||
![]() | Sulerythrin | ||||||
![]() | OXIDOREDUCTASE / sulerythrin / Hydrogen peroxide / molecular oxygen / bi-metallic binding site | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeoung, J.-H. / Dobbek, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation. Authors: Jeoung, J.H. / Runger, S. / Haumann, M. / Neumann, B. / Klemke, F. / Davis, V. / Fischer, A. / Dau, H. / Wollenberger, U. / Dobbek, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.6 KB | Display | ![]() |
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PDB format | ![]() | 117.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o89C ![]() 7o8aC ![]() 7o90C ![]() 7o91C ![]() 7o93C ![]() 7o99C ![]() 7o9cC ![]() 7o9dC ![]() 7o9eC ![]() 1j30S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16293.276 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST2370, STK_23700 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5) and 20-25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→38.96 Å / Num. obs: 108298 / % possible obs: 95.78 % / Redundancy: 9.75 % / CC1/2: 0.999 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.12→1.16 Å / Num. unique obs: 8223 / CC1/2: 0.486 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J30 Resolution: 1.12→38.96 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.406 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.031 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.41 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→38.96 Å
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Refine LS restraints |
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