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Yorodumi- PDB-6bzz: Crystal structure of halogenase PltM in complex with partially bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bzz | ||||||
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Title | Crystal structure of halogenase PltM in complex with partially bound FAD | ||||||
Components | (Halogenase PltM) x 2 | ||||||
Keywords | FLAVOPROTEIN / Halogenase / Chlorinase / Brominase / Iodinase | ||||||
Function / homology | alkylhalidase / alkylhalidase activity / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Halogenase PltM Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 6bzz.cif.gz | 405 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bzz.ent.gz | 326 KB | Display | PDB format |
PDBx/mmJSON format | 6bzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzz ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzz | HTTPS FTP |
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-Related structure data
Related structure data | 6bzaC 6bziC 6bznSC 6bzqC 6bztC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 58349.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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: Protein | Mass: 58397.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N terminal sequence is the 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 #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-CA / #5: 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: 2.3 Å3/Da / Density % sol: 46.5 % |
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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, soaked in same with 0.5 mM FAD |
-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: Jun 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 132527 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.8 / Num. unique obs: 6252 / CC1/2: 0.786 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BZN Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.186 / 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: 21.512 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→40 Å
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Refine LS restraints |
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