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- PDB-5k56: Human muscle fructose-1,6-bisphosphatase in active R-state in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k56 | ||||||
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Title | Human muscle fructose-1,6-bisphosphatase in active R-state in complex with fructose-1,6-bisphosphate | ||||||
![]() | Fructose-1,6-bisphosphatase isozyme 2 | ||||||
![]() | HYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle izozyme / FBPase / R-state / Leucine lock / F16BP | ||||||
Function / homology | ![]() sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural studies of human muscle FBPase Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D. #1: ![]() Title: Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase. Authors: Zarzycki, M. / Kolodziejczyk, R. / Maciaszczyk-Dziubinska, E. / Wysocki, R. / Jaskolski, M. / Dzugaj, A. #2: ![]() Title: Crystal structures of human muscle fructose-1,6-bisphosphatase: novel quaternary states, enhanced AMP affinity, and allosteric signal transmission pathway. Authors: Shi, R. / Chen, Z.Y. / Zhu, D.W. / Li, C. / Shan, Y. / Xu, G. / Lin, S.X. #3: ![]() Title: T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure. Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.9 KB | Display | ![]() |
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PDB format | ![]() | 137.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.8 KB | Display | ![]() |
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Full document | ![]() | 802.1 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k54C ![]() 5k55C ![]() 5l0aC ![]() 5et5S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36666.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: V85L IS A NATURAL VARIANT OF FBP2 Gaps in the sequence indicate residues that were not modeled because of poor electron density Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-FBP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 10mM magnesium chloride, 2M sodium chloride, 10% PEG6000, 10mM Tris PH range: 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: Jan 22, 2010 |
Radiation | Monochromator: Double crystal monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8943 Å / Relative weight: 1 |
Reflection | Resolution: 2.198→34.65 Å / Num. obs: 16183 / % possible obs: 98.8 % / Redundancy: 9.58 % / Biso Wilson estimate: 47.51 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.03 |
Reflection shell | Resolution: 2.198→2.33 Å / Redundancy: 9.48 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 3.55 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ET5 Resolution: 2.198→34.641 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.198→34.641 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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