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- PDB-1c80: REGULATORY COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1c80
TitleREGULATORY COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE
ComponentsFRUCTOSE-2,6-BISPHOSPHATASE
KeywordsHYDROLASE / Rossmann fold
Function / homology
Function and homology information


positive regulation of glycolytic process through fructose-6-phosphate / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / carbohydrate phosphorylation ...positive regulation of glycolytic process through fructose-6-phosphate / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / carbohydrate phosphorylation / fructose metabolic process / response to glucagon / negative regulation of glycolytic process through fructose-6-phosphate / response to starvation / animal organ regeneration / response to glucocorticoid / response to cAMP / response to insulin / kinase binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLee, Y.H. / Olson, T.W. / McClard, R.W. / Witte, J.F. / McFarlan, S.C. / Banaszak, L.J. / Levitt, D.G. / Lange, A.J.
Citation
Journal: To be Published
Title: Reaction Mechanism of Fructose-2,6-bisphosphatase Suggested by the Crystal Structures of a pseudo-Michaelis complex and Metabolite Complexes
Authors: Lee, Y.-H. / Olson, T.W. / McClard, R.W. / Witte, J.F. / McFarlan, S.C. / Banaszak, L.J. / Levitt, D.G. / Lange, A.J.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of a Trapped Phosphoenzyme During a Catalytic Reaction
Authors: Lee, Y.H. / Olson, T.W. / Ogata, C.M. / Levitt, D.G. / Banaszak, L.J. / Lange, A.J.
History
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Jul 7, 2021Group: Advisory / Derived calculations / Refinement description
Category: pdbx_validate_close_contact / refine / struct_site
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRUCTOSE-2,6-BISPHOSPHATASE
B: FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5956
Polymers44,3592
Non-polymers1,2364
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.8, 51.6, 79.9
Angle α, β, γ (deg.)90, 126.1, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FRUCTOSE-2,6-BISPHOSPHATASE


Mass: 22179.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PET3 / Production host: Escherichia coli (E. coli)
References: UniProt: P07953, fructose-2,6-bisphosphate 2-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Details: Guanosine-5'-triphosphate
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Details: inorganic phosphate / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.25
Details: PEG 4000, sodium chloride, Hepes, pH 7.25, EVAPORATION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9875
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.2→18 Å / Num. obs: 19365 / % possible obs: 94.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5 / Redundancy: 4.7 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.2→18 Å / σ(F): 1 / σ(I): 5 / Stereochemistry target values: Engh & Huber / Details: weighted matrix least squares procedure
RfactorNum. reflection% reflection
Rfree0.265 1947 -
Rwork0.201 --
all-19365 -
obs-17417 85.2 %
Refinement stepCycle: LAST / Resolution: 2.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 74 273 3457
Refine LS restraintsType: x_bond_d / Dev ideal: 0.02

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