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Yorodumi- PDB-1yz0: R-State AMP Complex Reveals Initial Steps of the Quaternary Trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yz0 | ||||||
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Title | R-State AMP Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-bisphosphatase | ||||||
Components | Fructose-1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / Allosteric enzymes / Intermediate states / glycolysis / 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 / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Iancu, C.V. / Mukund, S. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: R-state AMP complex reveals initial steps of the quaternary transition of fructose-1,6-bisphosphatase. Authors: Iancu, C.V. / Mukund, S. / 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 | 1yz0.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yz0.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yz0_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1yz0_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1yz0_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 1yz0_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yz0 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yz0 | HTTPS FTP |
-Related structure data
Related structure data | 1yxiC 1yyzC 1eykS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36733.289 Da / Num. of mol.: 2 / Mutation: A54L Source method: isolated from a genetically manipulated source Details: R-state / Source: (gene. exp.) Sus scrofa (pig) / Gene: FBP1, FBP / Production host: Escherichia coli (E. coli) / Strain (production host): DF 657 / References: UniProt: P00636, fructose-bisphosphatase #2: Sugar | #3: Chemical | #4: Chemical | #5: 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: 2.5 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: A54L FBPase (10mg/ml), 25mM Hepes pH7.4, 5 mM MgCl2, 5mM F16P2, 5mM AMP and a precipitant solution [Hepes (100mM, pH 7.4), PEG 3350 (14% w/v), 2-methyl-2,4-pentanediol (21% v/v), and t- ...Details: A54L FBPase (10mg/ml), 25mM Hepes pH7.4, 5 mM MgCl2, 5mM F16P2, 5mM AMP and a precipitant solution [Hepes (100mM, pH 7.4), PEG 3350 (14% w/v), 2-methyl-2,4-pentanediol (21% v/v), and t-butanol (5% v/v)], VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2001 / Details: CuKalpha Osmic confocal image system |
Radiation | Monochromator: CuKalpha radiation from Osmic confocal optics Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.38 Å / Num. all: 53756 / Num. obs: 53756 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EYK Resolution: 2.07→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 159651.46 / Data cutoff low absF: 0 / 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: 131.077 Å2 / ksol: 0.840237 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.07→2.19 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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