+Open data
-Basic information
Entry | Database: PDB / ID: 6ch6 | ||||||
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Title | Dehaloperoxidase B in complex with substrate 2,4-dimethoxyphenol | ||||||
Components | Dehaloperoxidase B | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | de Serrano, V.S. / Carey, L.M. / Ghiladi, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Peroxidase versus Peroxygenase Activity: Substrate Substituent Effects as Modulators of Enzyme Function in the Multifunctional Catalytic Globin Dehaloperoxidase. Authors: McGuire, A.H. / Carey, L.M. / de Serrano, V. / Dali, S. / 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 | 6ch6.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ch6.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6ch6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ch6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6ch6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ch6_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 6ch6_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6ch6 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6ch6 | HTTPS FTP |
-Related structure data
Related structure data | 6ch5C 6ckeC 6co5C 6creC 3ixfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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) / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 297 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-F0J / | #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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 32% PEG 3350, 0.2 M ammonium sulfate, 20 mM sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 12, 2017 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.23 Å / Num. obs: 29059 / % possible obs: 99.97 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.722 / Rpim(I) all: 0.065 / Rrim(I) all: 0.156 / Net I/σ(I): 13.81 |
Reflection shell | Resolution: 1.7→37.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / Num. unique obs: 2117 / CC1/2: 0.748 / Rpim(I) all: 0.309 / Rrim(I) all: 0.719 / % possible all: 99.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IXF Resolution: 1.7→37.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.952 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.027 / 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: 15.617 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→37.23 Å
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Refine LS restraints |
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