+Open data
-Basic information
Entry | Database: PDB / ID: 6onk | ||||||
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Title | Dehaloperoxidase B in complex with substrate 4-Cl-cresol | ||||||
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: 1.5 Å | ||||||
Authors | Ghiladi, R.A. / de Serrano, V.S. / Malewschik, T. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2019 Title: The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants. Authors: Malewschik, T. / de Serrano, V. / McGuire, A.H. / 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 | 6onk.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6onk.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 6onk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6onk_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6onk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6onk_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6onk_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/6onk ftp://data.pdbj.org/pub/pdb/validation_reports/on/6onk | HTTPS FTP |
-Related structure data
Related structure data | 6ongC 6onrC 6onxC 6onzC 6oo1C 6oo6C 6oo8C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) / Plasmid: pET16b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS AG / References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 280 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulphate, sodium 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: Feb 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.65 Å / Num. obs: 40677 / % possible obs: 97.88 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.051 / Rrim(I) all: 0.099 / Χ2: 1.056 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2502 / CC1/2: 0.751 / Rpim(I) all: 0.282 / Rrim(I) all: 0.47 / % possible all: 82.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.427 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.315 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→47.65 Å
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Refine LS restraints |
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