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- PDB-7t9d: Crystal structure of dehaloperoxidase B in complex with -(-) limo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t9d | ||||||
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Title | Crystal structure of dehaloperoxidase B in complex with -(-) limonene oxide | ||||||
![]() | Dehaloperoxidase B | ||||||
![]() | OXIDOREDUCTASE / dehaloperoxidase B / heme peroxidase / peroxigenase / oxygen binding / heme cofactor | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Serran, V.S. / Ghiladi, R.A. / Malewschik, T. / Yun, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes Authors: Malewschik, T. / de Serrano, V. / Yun, D. / 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 | ![]() | 144.8 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sjbC ![]() 7sjcC ![]() 7sjdC ![]() 7sjeC ![]() 7sjfC ![]() 7sjgC ![]() 7sjhC ![]() 7sjiC ![]() 7t9cC ![]() 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 , 5 types, 148 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GHI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GHI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: 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: 2.16 Å3/Da / Density % sol: 43.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / 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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→34.193 Å / Num. obs: 31407 / % possible obs: 97.3 % / Redundancy: 3.7 % / CC1/2: 0.975 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.66→1.703 Å / Num. unique obs: 2247 / CC1/2: 0.447 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IXF Resolution: 1.66→34.193 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.701 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.123 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: 24.037 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→34.193 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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