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Open data
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Basic information
Entry | Database: PDB / ID: 6onr | ||||||
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Title | Dehaloperoxidase B in complex with substrate 4-methyl-cresol | ||||||
![]() | Dehaloperoxidase B | ||||||
![]() | OXIDOREDUCTASE / heme peroxydase / peroxygenase / heme cofactor | ||||||
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. | ||||||
![]() | ![]() Title: The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants. Authors: Malewschik, T. / de Serrano, V. / McGuire, A.H. / 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 | ![]() | 169 KB | Display | ![]() |
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PDB format | ![]() | 134.5 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 | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ongC ![]() 6onkC ![]() 6onxC ![]() 6onzC ![]() 6oo1C ![]() 6oo6C ![]() 6oo8C ![]() 3ixfS 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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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, 360 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/N0D.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/N0D.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulphate, sodium 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: Feb 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→37.22 Å / Num. obs: 56853 / % possible obs: 99.45 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.046 / Χ2: 1.012 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.35→1.385 Å / Redundancy: 2.9 % / Num. unique obs: 4091 / CC1/2: 0.82 / Rpim(I) all: 0.243 / Rrim(I) all: 0.438 / Χ2: 0.707 / % possible all: 96.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IXF Resolution: 1.35→37.22 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.052 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.053 / 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: 14.848 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→37.22 Å
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Refine LS restraints |
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