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- PDB-1nf8: Crystal structure of PhzD protein active site mutant with substrate -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nf8 | ||||||
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Title | Crystal structure of PhzD protein active site mutant with substrate | ||||||
![]() | phenazine biosynthesis protein phzD | ||||||
![]() | HYDROLASE / isochorismatase / enzyme / phenazine pathway | ||||||
Function / homology | ![]() trans-2,3-dihydro-3-hydroxyanthranilic acid synthase / isochorismatase activity / phenazine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Parsons, F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 628.9 KB | Display | ![]() |
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Full document | ![]() | 630.6 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 assembly is generated by the two fold axis: -x,y,-z+3/2 |
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Components
#1: Protein | Mass: 23176.529 Da / Num. of mol.: 1 / Mutation: D38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7DC80, UniProt: P0DPB9*PLUS, isochorismatase |
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#2: Sugar | ChemComp-BOG / |
#3: Chemical | ChemComp-ISC / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 47.45 % | ||||||||||||||||||||||||||||||
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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 isochorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 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: 1.6→20 Å / Num. obs: 27572 / % possible obs: 99.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3895 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 82842 |
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Native structure Resolution: 1.6→20 Å / Num. parameters: 17662 / Num. restraintsaints: 21130 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1608 / Occupancy sum non hydrogen: 1962 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→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: 1.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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