+Open data
-Basic information
Entry | Database: PDB / ID: 7o89 | ||||||
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Title | sulerythrin without metals (apo-state) | ||||||
Components | Sulerythrin | ||||||
Keywords | OXIDOREDUCTASE / sulerythrin / Hydrogen peroxide / molecular oxygen / bi-metallic binding site | ||||||
Function / homology | Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily / oxidoreductase activity / metal ion binding / Sulerythrin Function and homology information | ||||||
Biological species | Sulfurisphaera tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||
Authors | Jeoung, J.-H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Inorg.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o89.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o89.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 7o89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o89_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 7o89_full_validation.pdf.gz | 429.4 KB | Display | |
Data in XML | 7o89_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 7o89_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/7o89 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/7o89 | HTTPS FTP |
-Related structure data
Related structure data | 7o8aC 7o8dC 7o90C 7o91C 7o93C 7o99C 7o9cC 7o9dC 7o9eC 1j30S 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16098.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST2370, STK_23700 / Production host: Escherichia coli B (bacteria) / References: UniProt: F9VPE5 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.22 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→48.07 Å / Num. obs: 974906 / % possible obs: 99.92 % / Redundancy: 12.81 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.16→1.2 Å / Num. unique obs: 7457 / CC1/2: 0.617 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J30 Resolution: 1.16→48.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.799 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / 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: 16.954 Å2
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Refinement step | Cycle: 1 / Resolution: 1.16→48.07 Å
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Refine LS restraints |
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