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- PDB-7sjd: Crystal structure of dehaloperoxidase B in complex with terpinolene -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sjd | ||||||
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Title | Crystal structure of dehaloperoxidase B in complex with terpinolene | ||||||
![]() | 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. / Yun, D. / Malewschik, T. | ||||||
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 | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 100.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sjbC ![]() 7sjcC ![]() 7sjeC ![]() 7sjfC ![]() 7sjgC ![]() 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 , 5 types, 120 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/9LR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/9LR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | LIGAND 9LR OCCUPIES DENSITY THAT IS CLOSE TO THE POSITION OF H55 IN ITS ALTERNATE CONFORMATION. THE ...LIGAND 9LR OCCUPIES DENSITY THAT IS CLOSE TO THE POSITION OF H55 IN ITS ALTERNATE CONFORMATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
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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: 1.7→37.383 Å / Num. obs: 30227 / % possible obs: 98.52 % / Redundancy: 4.6 % / CC1/2: 0.996 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.703→1.748 Å / Num. unique obs: 1853 / CC1/2: 0.547 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IXF Resolution: 1.703→37.383 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.479 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 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: 31.851 Å2
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Refinement step | Cycle: LAST / Resolution: 1.703→37.383 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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