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- PDB-8ejn: Structure of dehaloperoxidase A in complex with 2,4-dichlorophenol -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ejn | ||||||
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Title | Structure of dehaloperoxidase A in complex with 2,4-dichlorophenol | ||||||
![]() | Dehaloperoxidase A | ||||||
![]() | OXIDOREDUCTASE / peroxidase / peroxygenase / oxydation / substrate / heme / cofactor / oxygen binding | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aktar, M.S. / de Serrano, V.S. / Franzen, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B. Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R. / Franzen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.1 KB | Display | ![]() |
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PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ew6S S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15548.597 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 330 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/5JC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5JC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Nonpolymer details | In chain A internal conformation of H55 (conformation A) is not possible when the substrate is ...In chain A internal conformation of H55 (conformation A) is not possible when the substrate is bound. When the substrate (5JC) is bound His55 is oriented such that it is facing outside of the heme pocket, and it cannot be present inside because the substrate is bound close to the area where Hiss55 would be otherwise located. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 27-33% PEG 4000, 0.2 M Ammonium Sulfate, 0.020 M Sodium Cacodylate, pH 6.0-6.5 |
-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: Sep 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→37.091 Å / Num. obs: 44772 / % possible obs: 98.03 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.481→1.519 Å / Rmerge(I) obs: 0.641 / Num. unique obs: 3047 / CC1/2: 0.701 / Rpim(I) all: 0.369 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EW6 Resolution: 1.481→37.091 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.812 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.082 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: 13.254 Å2
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Refinement step | Cycle: LAST / Resolution: 1.481→37.091 Å
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Refine LS restraints |
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LS refinement shell |
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