+Open data
-Basic information
Entry | Database: PDB / ID: 1nf9 | ||||||
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Title | Crystal Structure of PhzD protein from Pseudomonas aeruginosa | ||||||
Components | phenazine biosynthesis protein phzD | ||||||
Keywords | HYDROLASE / isochorismatase / enzyme / phenazine pathway | ||||||
Function / homology | Function and homology information trans-2,3-dihydro-3-hydroxyanthranilic acid synthase / isochorismatase activity / phenazine biosynthetic process Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD S / Resolution: 1.5 Å | ||||||
Authors | Parsons, F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway Authors: Parsons, J.F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nf9.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nf9.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nf9_validation.pdf.gz | 644.8 KB | Display | wwPDB validaton report |
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Full document | 1nf9_full_validation.pdf.gz | 648.4 KB | Display | |
Data in XML | 1nf9_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1nf9_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf9 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf9 | 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 on special symmetry positions |
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Details | The second part of the biological dimer is generated by the two fold axis: -x,y,-z+3/2 |
-Components
#1: Protein | Mass: 23220.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PhzD / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) References: UniProt: Q7DC80, UniProt: P0DPB9*PLUS, isochorismatase |
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#2: Sugar | ChemComp-BOG / |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 47.78 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-20% polyethylene glycol 4000, 0.2M ammonium formate, 0.2% beta-octylglucoside, 1mM aminodeoxychorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2002 / Details: OSMIC |
Radiation | Monochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 33819 / Num. obs: 33819 / % possible obs: 92.7 % / Redundancy: 11 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 3.2 / % possible all: 80.4 |
Reflection | *PLUS Num. measured all: 357616 |
Reflection shell | *PLUS % possible obs: 80.4 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD S / Resolution: 1.5→20 Å / Num. parameters: 17525 / Num. restraintsaints: 20980 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R BY 0.035
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1607 / Occupancy sum non hydrogen: 1945.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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