[English] 日本語
Yorodumi- PDB-1nf8: Crystal structure of PhzD protein active site mutant with substrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nf8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PhzD protein active site mutant with substrate | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nf8.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nf8.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 1nf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nf8_validation.pdf.gz | 628.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1nf8_full_validation.pdf.gz | 630.6 KB | Display | |
Data in XML | 1nf8_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1nf8_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf8 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The second part of the biological assembly is generated by the two fold axis: -x,y,-z+3/2 |
-Components
#1: Protein | Mass: 23176.529 Da / Num. of mol.: 1 / Mutation: D38A 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 |
---|---|
#2: Sugar | ChemComp-BOG / |
#3: Chemical | ChemComp-ISC / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 47.45 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
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 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1608 / Occupancy sum non hydrogen: 1962 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
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
|