[English] 日本語
Yorodumi- PDB-1n8f: Crystal structure of E24Q mutant of phenylalanine-regulated 3-deo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n8f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E24Q mutant of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Escherichia Coli in complex with Mn2+ and PEP | ||||||
Components | DAHP Synthetase | ||||||
Keywords | METAL BINDING PROTEIN / (Beta/Alpha)8 Barrel | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Shumilin, I.A. / Bauerle, R. / Kretsinger, R.H. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: The High-Resolution Structure of 3-Deoxy-D-arabino-heptulosonate-7-phosphate Synthase Reveals a Twist in the Plane of Bound Phosphoenolpyruvate Authors: Shumilin, I.A. / Bauerle, R. / Kretsinger, R.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n8f.cif.gz | 299.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n8f.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n8f ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8f | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly of the wild type DAHP synthase is a tetramer similar to the one located in the asymmetric unit of E24Q mutant. |
-Components
#1: Protein | Mass: 38058.520 Da / Num. of mol.: 4 / Mutation: E24Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AroG / Plasmid: pTAG29 / Production host: Escherichia coli (E. coli) / Strain (production host): CB961 / References: UniProt: P0AB91, EC: 4.1.2.15 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEP / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.57 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: PEG4000, manganese sulfate, phosphoenolpyruvate, lithium sulfate, bis-tris propane, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2001 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 152257 / Num. obs: 151346 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
| |||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 2 % | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|