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- PDB-8q22: Crystal structure of Vanadium-dependent haloperoxidase R425S muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q22 | ||||||
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Title | Crystal structure of Vanadium-dependent haloperoxidase R425S mutant in complex with 1,3,5-trimethoxybenzene (A. marina) | ||||||
![]() | Vanadium-dependent bromoperoxidase, putative | ||||||
![]() | OXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation / Mutant / Ligand-Complex | ||||||
Function / homology | Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / peroxidase activity / : / PHOSPHATE ION / Vanadium-dependent bromoperoxidase, putative![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Unraveling the Molecular Basis of Substrate Specificity and Halogen Activation in Vanadium-Dependent Haloperoxidases Authors: Zeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.5 KB | Display | ![]() |
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PDB format | ![]() | 210.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8q20C ![]() 8q21C 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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Unit cell |
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Components
#1: Protein | Mass: 73040.531 Da / Num. of mol.: 1 / Mutation: R452S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-ILW / Mass: 168.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O3 / Feature type: SUBJECT OF INVESTIGATION | ||
#4: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS, 1.25 M ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate, 10 mM 1,3,5-trimethoxybenzene |
-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 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 17934 / % possible obs: 94.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.3→3.4 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2 / Num. unique obs: 1528 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 142.82 Å2 / Biso mean: 83.809 Å2 / Biso min: 70.71 Å2
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Refinement step | Cycle: final / Resolution: 3.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.3154 Å / Origin y: 4.7758 Å / Origin z: 44.4646 Å
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