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Yorodumi- PDB-1nv2: Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nv2 | ||||||
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Title | Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Phosphate, Phosphate and Thallium (20 mM) | ||||||
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: 2.1 Å | ||||||
Authors | Choe, J. / Iancu, C.V. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Interaction of Tl+ with product complexes of fructose-1,6-bisphosphatase Authors: Choe, J.Y. / Nelson, S.W. / 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 | 1nv2.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nv2.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nv2_validation.pdf.gz | 798.9 KB | Display | wwPDB validaton report |
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Full document | 1nv2_full_validation.pdf.gz | 810.2 KB | Display | |
Data in XML | 1nv2_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1nv2_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nv2 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nv2 | HTTPS FTP |
-Related structure data
Related structure data | 1nuzC 1nv0C 1nv1C 1nv3C 1nv4C 1nv5C 1nv6C 1nv7C 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
-Protein / Sugars , 2 types, 2 molecules A
#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 / |
-Non-polymers , 5 types, 236 molecules
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-PI / | #6: Chemical | ChemComp-TL / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | MG A2341 AND TL A2342 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. MG A2343 AND TL A2344 ARE IN ...MG A2341 AND TL A2342 ARE IN ALTERNATE CONFORMATI |
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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: 2.3 Å3/Da / Density % sol: 46.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 3350, HEPES, pH 7.4, 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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: May 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 17604 / Num. obs: 17604 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.03 |
Reflection shell | Resolution: 2.1→2.19 Å / % possible all: 43.7 |
Reflection | *PLUS Num. measured all: 92869 |
Reflection shell | *PLUS % possible obs: 43.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EYI Resolution: 2.1→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 15652 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2487 / Rfactor Rwork: 0.1703 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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