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Yorodumi- PDB-1q9d: Fructose-1,6-bisphosphatase Complexed with a New Allosteric Site ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q9d | ||||||
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Title | Fructose-1,6-bisphosphatase Complexed with a New Allosteric Site Inhibitor (I-State) | ||||||
Components | Fructose-1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / BISPHOSPHATASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Honzatko, R.B. / Choe, J.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors Authors: Choe, J.Y. / Nelson, S.W. / Arienti, K.L. / Axe, F.U. / Collins, T.L. / Jones, T.K. / Kimmich, R.D. / Newman, M.J. / Norvell, K. / Ripka, W.C. / Romano, S.J. / Short, K.M. / Slee, D.H. / ...Authors: Choe, J.Y. / Nelson, S.W. / Arienti, K.L. / Axe, F.U. / Collins, T.L. / Jones, T.K. / Kimmich, R.D. / Newman, M.J. / Norvell, K. / Ripka, W.C. / Romano, S.J. / Short, K.M. / Slee, D.H. / 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 | 1q9d.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q9d.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q9d_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1q9d_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1q9d_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1q9d_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q9d ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q9d | HTTPS FTP |
-Related structure data
Related structure data | 1eyjS 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 36691.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: liver / Production host: Escherichia coli (E. coli) / Strain (production host): DF657 / References: UniProt: P00636, fructose-bisphosphatase #2: Sugar | |
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-Non-polymers , 4 types, 301 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PO4 / #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: 2.58 Å3/Da / Density % sol: 51.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 3350, Tris-malonate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 16, 1999 |
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: 2.35→50 Å / Num. all: 32966 / Num. obs: 28849 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.35→2.45 Å / % possible all: 66 |
Reflection | *PLUS Num. measured all: 94949 |
Reflection shell | *PLUS Lowest resolution: 2.44 Å / % possible obs: 65.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EYJ Resolution: 2.35→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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