[English] 日本語
Yorodumi- PDB-1bk4: CRYSTAL STRUCTURE OF RABBIT LIVER FRUCTOSE-1,6-BISPHOSPHATASE AT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bk4 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF RABBIT LIVER FRUCTOSE-1,6-BISPHOSPHATASE AT 2.3 ANGSTROM RESOLUTION | ||||||
Components | PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE) | ||||||
Keywords | HYDROLASE / BISPHOSPHATASE | ||||||
Function / homology | Function and homology information cellular response to xenobiotic stimulus => GO:0071466 / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / cellular response to magnesium ion / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding ...cellular response to xenobiotic stimulus => GO:0071466 / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / cellular response to magnesium ion / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / gluconeogenesis / negative regulation of cell growth / metal ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å | ||||||
Authors | Ghosh, D. / Weeks, C.M. / Erman, M. / Roszak, A.W. / Kaiser, R. / Jornvall, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution. Authors: Weeks, C.M. / Roszak, A.W. / Erman, M. / Kaiser, R. / Jornvall, H. / Ghosh, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bk4.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bk4.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bk4 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bk4 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36490.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: LIVER / References: UniProt: P00637, fructose-bisphosphatase | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.4 Details: 10-15% PEG 4000, 50-200 MM A.S. IN 25 MM TRIS, pH 7.4 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 285 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Jan 15, 1990 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. obs: 16921 / % possible obs: 93 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.8 |
Reflection | *PLUS Num. measured all: 67887 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.3→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|