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Yorodumi- PDB-1nuw: Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nuw | ||||||
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Title | Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Phosphate and Phosphate at pH 9.6 | ||||||
Components | Fructose-1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / Bisphosphatase / Allosteric enzymes / Gluconeogenesis | ||||||
Function / homology | Function and homology information Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process ...Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Choe, J. / Iancu, C.V. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Metaphosphate in the active site of fructose-1,6-bisphosphatase Authors: Choe, J.Y. / Iancu, C.V. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nuw.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nuw.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nuw_validation.pdf.gz | 793 KB | Display | wwPDB validaton report |
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Full document | 1nuw_full_validation.pdf.gz | 803.5 KB | Display | |
Data in XML | 1nuw_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1nuw_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nuw ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nuw | HTTPS FTP |
-Related structure data
Related structure data | 1nuxC 1nuyC 1eyiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36691.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P00636, fructose-bisphosphatase | ||
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#2: Sugar | ChemComp-F6P / | ||
#3: Chemical | ChemComp-PO3 / | ||
#4: Chemical | ChemComp-MG / #5: 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: 2.35 Å3/Da / Density % sol: 47.23 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: PEG 3350, Glycine, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å |
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Detector | Type: SBC / Detector: CCD / Date: Jun 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 90683 / Num. obs: 84282 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.024 |
Reflection shell | Resolution: 1.3→1.35 Å / % possible all: 65.8 |
Reflection | *PLUS Num. obs: 83972 / Num. measured all: 347535 |
Reflection shell | *PLUS Highest resolution: 1.3 Å / % possible obs: 65.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EYI Resolution: 1.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 77354 / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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