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Yorodumi- PDB-1eyi: FRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eyi | ||||||
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Title | FRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE AND PHOSPHATE (R-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 / 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: 2.32 Å | ||||||
Authors | Choe, J. / Honzatko, R.B. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes. Authors: Choe, J.Y. / 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 | 1eyi.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyi.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 1eyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eyi_validation.pdf.gz | 393 KB | Display | wwPDB validaton report |
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Full document | 1eyi_full_validation.pdf.gz | 400.8 KB | Display | |
Data in XML | 1eyi_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1eyi_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyi ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyi | HTTPS FTP |
-Related structure data
Related structure data | 1eyjC 1eykC 1cnqS 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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Unit cell |
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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) / Tissue: LIVER / Plasmid: DF657 / Production host: Escherichia coli (E. coli) / References: UniProt: P00636, fructose-bisphosphatase | ||||
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#2: Sugar | ChemComp-F6P / | ||||
#3: Chemical | #4: Chemical | #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: 2.4 Å3/Da / Density % sol: 48.44 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.4 Details: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS Crystal-ID: 1
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 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: 2.32→50 Å / Num. all: 31247 / Num. obs: 30028 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.64 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.32→2.46 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.239 / Num. unique all: 3557 / % possible all: 75.5 |
Reflection | *PLUS Num. measured all: 72680 |
Reflection shell | *PLUS % possible obs: 75.5 % |
-Processing
Software |
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Refinement | Starting model: 1CNQ Resolution: 2.32→5 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 132.213 Å2 / ksol: 1.47526 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.32→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.45 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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