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Yorodumi- PDB-1fj9: FRUCTOSE-1,6-BISPHOSPHATASE (MUTANT Y57W) PRODUCTS/ZN/AMP COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fj9 | ||||||
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Title | FRUCTOSE-1,6-BISPHOSPHATASE (MUTANT Y57W) PRODUCTS/ZN/AMP COMPLEX (T-STATE) | ||||||
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 / fructose 1,6-bisphosphate metabolic 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 / fructose 1,6-bisphosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Iancu, C.V. / Choe, J.Y. / Honzatko, R.B. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Tryptophan fluorescence reveals the conformational state of a dynamic loop in recombinant porcine fructose-1,6-bisphosphatase. Authors: Nelson, S.W. / Iancu, C.V. / Choe, J.Y. / Honzatko, R.B. / Fromm, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fj9.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fj9.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/1fj9 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/1fj9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 36714.246 Da / Num. of mol.: 2 / Mutation: Y57W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: KIDNEY / Production host: Escherichia coli (E. coli) / References: UniProt: P00636, fructose-bisphosphatase #2: Sugar | |
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-Non-polymers , 4 types, 224 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3350, MPD, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. all: 88507 / Num. obs: 79656 / % possible obs: 90 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / % possible all: 83 |
Reflection | *PLUS Num. all: 79656 / Num. obs: 25328 / Num. measured all: 88507 |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ieyj Resolution: 2.5→5 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: flat model / Bsol: 93.2934 Å2 / ksol: 1.05446 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.63 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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