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Open data
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Basic information
Entry | Database: PDB / ID: 7sjg | ||||||
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Title | Structure of Dehaloperoxidase B in Complex with Thymoquinone | ||||||
![]() | Dehaloperoxidase B | ||||||
![]() | OXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghiladi, R.A. / de Serrano, V.S. / Malewschik, T. / Yun, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes Authors: Malewschick, T. / Yun, D. / de Serrano, V. / Ghiladi, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.2 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.3 MB | Display | ![]() |
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Full document | ![]() | 5.2 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sjbC ![]() 7sjcC ![]() 7sjdC ![]() 7sjeC ![]() 7sjfC ![]() 7sjhC ![]() 7sjiC ![]() 7t9cC ![]() 7t9dC ![]() 7t9eC ![]() 3ixfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15414.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 224 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/9J9.gif)
![](data/chem/img/9IX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/9J9.gif)
![](data/chem/img/9IX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-9J9 / ( #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | Ligand 9J9 occupies density that is close to the position of H55 in its alternate conformation. The ...Ligand 9J9 occupies density that is close to the position of H55 in its alternate conformation. The occupancies of the alternate conformations reflect the fact. In the fraction where the ligand is bound, reflected by the occupancy of the ligand, H55 is in the conformation facing outside of the distal side of the heme pocket, with the same occupancy as the bound ligand. When the ligand is not bound, H55 can occupy the inside conformation, also reflected by its occupancy. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulfate, Na cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.2 Å / Num. obs: 53478 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.4→1.436 Å / Num. unique obs: 3750 / CC1/2: 0.541 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IXF Resolution: 1.4→44.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.415 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.068 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→44.2 Å
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Refine LS restraints |
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LS refinement shell |
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