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Yorodumi- PDB-4hmu: Crystal structure of PhzG from Pseudomonas fluorescens 2-79 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hmu | ||||||
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Title | Crystal structure of PhzG from Pseudomonas fluorescens 2-79 in complex with tetrahydrophenazine-1-carboxylic acid after 1 day of soaking | ||||||
Components | Phenazine biosynthesis protein phzG | ||||||
Keywords | OXIDOREDUCTASE / phenazine biosynthesis / trapping / intermediate | ||||||
Function / homology | Function and homology information dihydrophenazinedicarboxylate synthase / phenazine biosynthetic process / pyridoxamine phosphate oxidase activity / pyridoxine biosynthetic process / FMN binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å | ||||||
Authors | Xu, N.N. / Ahuja, E.G. / Blankenfeldt, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis Authors: Xu, N. / Ahuja, E.G. / Janning, P. / Mavrodi, D.V. / Thomashow, L.S. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hmu.cif.gz | 278 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hmu.ent.gz | 228.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hmu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4hmu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4hmu_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4hmu_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/4hmu ftp://data.pdbj.org/pub/pdb/validation_reports/hm/4hmu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25249.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: 2-79 / Gene: phzG / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS References: UniProt: Q51793, Oxidoreductases; Acting on the CH-NH2 group of donors #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-WUB / ( | #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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 21-24% (w/v) PEG 3350, 0.2M (NH4)2SO4, 0.1M BisTris, 15uM PhzF, 30 uM PhzA/B, 0.2M TRIS-HCl pH 7.5, vapor diffusion, hanging drop, temperature 298K PH range: 6.2-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98004 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98004 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→44 Å / Num. obs: 69696 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→43.46 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.13 / σ(F): 1.91 / Phase error: 13.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.22 Å2 / Biso mean: 26.4136 Å2 / Biso min: 8.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→43.46 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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