+Open data
-Basic information
Entry | Database: PDB / ID: 6ch5 | ||||||
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Title | Dehaloperoxidase B in complex with substrate 4-Nitroguaiacol | ||||||
Components | Dehaloperoxidase B | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 6ch5.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ch5.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ch5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6ch5 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6ch5 | HTTPS FTP |
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-Related structure data
Related structure data | 6ch6C 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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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 , 6 types, 272 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-F0M / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, ammonium sulfate,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 / Details: double-crystal monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44.36 Å / Num. obs: 31440 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.776 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.326 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IXF Resolution: 1.65→44.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.318 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.023 / 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: 13.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→44.36 Å
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Refine LS restraints |
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