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Yorodumi- PDB-6bza: Crystal structure of halogenase PltM in complex with phloroglucin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bza | ||||||
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Title | Crystal structure of halogenase PltM in complex with phloroglucinol and FAD | ||||||
Components | Halogenase PltM | ||||||
Keywords | FLAVOPROTEIN / Halogenase / Chlorinase / Brominase / Iodinase | ||||||
Function / homology | Function and homology information alkylhalidase / monooxygenase activity / hydrolase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 6bza.cif.gz | 396.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bza.ent.gz | 319.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bza ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bza | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.: 4 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: Chemical | #3: Chemical | #4: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8, 0.2 M NaCl, 0.1 M CaCl2 and 12-17% PEG 8000; after growth soak in the same solution with 0.5 mM FAD and 1 mM phloroglucinol PH range: 8 |
-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 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 65800 / % possible obs: 98.9 % / Observed criterion σ(I): 2.17 / Redundancy: 6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 14.04 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.663 / Num. unique obs: 3267 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.656 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / 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: 46.642 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→40 Å
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