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Yorodumi- PDB-5fbp: CRYSTAL STRUCTURE OF THE NEUTRAL FORM OF FRUCTOSE-1,6-BISPHOSPHAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fbp | ||||||
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Title | CRYSTAL STRUCTURE OF THE NEUTRAL FORM OF FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH THE PRODUCT FRUCTOSE 6-PHOSPHATE AT 2.1-ANGSTROMS RESOLUTION | ||||||
Components | FRUCTOSE 1,6-BISPHOSPHATASE | ||||||
Keywords | HYDROLASE (PHOSPHORIC MONOESTER) | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Ke, H. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Crystal structure of the neutral form of fructose-1,6-bisphosphatase complexed with the product fructose 6-phosphate at 2.1-A resolution. Authors: Ke, H.M. / Zhang, Y.P. / Liang, J.Y. / Lipscomb, W.N. #1: Journal: Biochemistry / Year: 1991 Title: Conformational Transition of Fructose-1,6-Bisphosphatase: Structure Comparison between the AMP Complex (T Form) and the Fructose 6-Phosphate Complex (R Form) Authors: Ke, H. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbp.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbp.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fbp_validation.pdf.gz | 508.4 KB | Display | wwPDB validaton report |
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Full document | 5fbp_full_validation.pdf.gz | 514.8 KB | Display | |
Data in XML | 5fbp_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5fbp_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbp ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36503.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00636, fructose-bisphosphatase #2: Sugar | #3: Water | ChemComp-HOH / | Nonpolymer details | THERE IS A MOLECULE OF F6P BOUND AT THE ACTIVE SITE IN BOTH CHAINS. THERE IS A MOLECULE OF F6P ...THERE IS A MOLECULE OF F6P BOUND AT THE ACTIVE SITE IN BOTH CHAINS. THERE IS A MOLECULE OF F6P BOUND AT THE AMP SITE IN CHAIN *A* BUT NOT IN CHAIN *B*. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.04 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.4 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 38643 / % possible obs: 97 % / Num. measured all: 200580 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.177 / Highest resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Num. reflection all: 35069 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |