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Yorodumi- PDB-4hms: Crystal structure of PhzG from Pseudomonas fluorescens 2-79 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hms | ||||||
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Title | Crystal structure of PhzG from Pseudomonas fluorescens 2-79 in complex with a second FMN in the substrate binding site | ||||||
Components | Phenazine biosynthesis protein phzG | ||||||
Keywords | OXIDOREDUCTASE / excess FMN / substrate mimic | ||||||
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: 1.33 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 | 4hms.cif.gz | 291.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hms.ent.gz | 241.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/4hms ftp://data.pdbj.org/pub/pdb/validation_reports/hm/4hms | HTTPS FTP |
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-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 | ChemComp-SO4 / #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: 2.43 Å3/Da / Density % sol: 49.39 % / Mosaicity: 0 ° |
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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, 10mM FMN, pH 6.2-6.6, 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: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.271→19.285 Å / Num. obs: 113420 / % possible obs: 99.8 % / Redundancy: 3.9 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.33→19.278 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.937 / SU ML: 0.11 / σ(F): 1.91 / Phase error: 12.55 / 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: 62.42 Å2 / Biso mean: 17.3354 Å2 / Biso min: 3.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→19.278 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: 30
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