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Yorodumi- PDB-7m1k: Crystal structure of dehaloperoxidase B in complex with 2,6-diflu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m1k | ||||||
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Title | Crystal structure of dehaloperoxidase B in complex with 2,6-difluorophenol | ||||||
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: 1.795 Å | ||||||
Authors | Ghiladi, R.A. / de Serrano, V.S. / Malewschik, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Inorg.Biochem. / Year: 2022 Title: Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols. Authors: Malewschik, T. / Carey, L.M. / 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 | 7m1k.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m1k.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 7m1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/7m1k ftp://data.pdbj.org/pub/pdb/validation_reports/m1/7m1k | HTTPS FTP |
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-Related structure data
Related structure data | 7m1iC 7m1jC 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(DE3) (bacteria) / References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 43.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: ammonium sulfate, sodium cacodylate, MPEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→37.122 Å / Num. obs: 24292 / % possible obs: 94.22 % / Redundancy: 3.5 % / CC1/2: 0.994 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.795→1.842 Å / Num. unique obs: 1670 / CC1/2: 0.776 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ixf Resolution: 1.795→37.122 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.318 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.146 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: 20.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.795→37.122 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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