+Open data
-Basic information
Entry | Database: PDB / ID: 5dbj | ||||||
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Title | Crystal structure of halogenase PltA | ||||||
Components | FADH2-dependent halogenase PltA | ||||||
Keywords | FLAVOPROTEIN / halogenase / FAD / Rossmann fold / pyoluteorin | ||||||
Function / homology | Function and homology information 1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] chlorinase / alkylhalidase activity / antibiotic biosynthetic process / FAD binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Pang, A.H. / Tsodikov, O.V. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway. Authors: Pang, A.H. / 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 | 5dbj.cif.gz | 873.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dbj.ent.gz | 738.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dbj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5dbj_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5dbj_validation.xml.gz | 75.4 KB | Display | |
Data in CIF | 5dbj_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/5dbj ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dbj | HTTPS FTP |
-Related structure data
Related structure data | 3nixS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 51391.062 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) (bacteria) Strain: Pf-5 / ATCC BAA-477 / Gene: pltA, PFL_2787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCZ0, alkylhalidase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CL / #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: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane, pH 7.0, 50 mM magnesium sulfate heptahydrate, 20% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9786 Å |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Feb 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 56814 / % possible obs: 95.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.59 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NIX Resolution: 2.75→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 51.317 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.222 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→40 Å
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Refine LS restraints |
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