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Yorodumi- PDB-7sjh: Crystal structure of dehaloperoxidase B in complex with S-(-)-limonene -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sjh | ||||||
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Title | Crystal structure of dehaloperoxidase B in complex with S-(-)-limonene | ||||||
Components | Dehaloperoxidase B | ||||||
Keywords | OXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding | ||||||
Function / homology | Function and homology information oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Ghiladi, R.A. / de Serrano, V.S. / Malewschik, T. / Yun, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sjh.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sjh.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 7sjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/7sjh ftp://data.pdbj.org/pub/pdb/validation_reports/sj/7sjh | HTTPS FTP |
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-Related structure data
Related structure data | 7sjbC 7sjcC 7sjdC 7sjeC 7sjfC 7sjgC 7sjiC 7t9cC 7t9dC 7t9eC 3ixfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold(DE3) / References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 123 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | Ligand 9IU occupies density that is close to the position of H55 in its alternate conformation. The ...Ligand 9IU occupies density that is close to the position of H55 in its alternate conformation. The occupancies of the alternate conformations reflect the fact. In the fraction where the ligand is bound, reflected by the occupancy of the ligand, H55 is in the conformation facing outside of the distal side of the heme pocket, with the same occupancy as the bound ligand. When the ligand is not bound, H55 can occupy the inside conformation, also reflected by its occupancy. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
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: 1.87→37.38 Å / Num. obs: 22814 / % possible obs: 97.91 % / Redundancy: 4.7 % / CC1/2: 0.989 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.87→1.918 Å / Num. unique obs: 1621 / CC1/2: 0.846 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IXF Resolution: 1.87→37.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.97 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.155 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: 34.874 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→37.38 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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