+Open data
-Basic information
Entry | Database: PDB / ID: 6bzn | ||||||
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Title | Crystal structure of halogenase PltM | ||||||
Components | Halogenase PltM | ||||||
Keywords | FLAVOPROTEIN / Halogenase / Chlorinase / Brominase / Iodinase | ||||||
Function / homology | alkylhalidase / alkylhalidase activity / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / Halogenase PltM Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pang, A.H. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Unusual substrate and halide versatility of phenolic halogenase PltM. Authors: Mori, S. / Pang, A.H. / Thamban Chandrika, N. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bzn.cif.gz | 446.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bzn.ent.gz | 356.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzn ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzn | HTTPS FTP |
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-Related structure data
Related structure data | 6bzaC 6bziSC 6bzqC 6bztC 6bzzC 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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Unit cell |
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-Components
#1: Protein | Mass: 58349.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The N-terminal sequence is a cloning tag Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltM, PFL_2784 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4KCZ3, alkylhalidase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: 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: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris pH 8, 0.2 M NaCl, 0.1 M CaCl2 and 12-17% PEG 8000, crystals frozen in the same solution additionally containing 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 200457 / % possible obs: 99.5 % / Observed criterion σ(I): 1.7 / Redundancy: 6.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.766 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BZI Resolution: 1.8→39.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.653 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.106 / 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: 20.314 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→39.88 Å
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Refine LS restraints |
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