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- PDB-1fpi: FRUCTOSE-1,6-BISPHOSPHATASE (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPH... -

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Basic information

Entry
Database: PDB / ID: 1fpi
TitleFRUCTOSE-1,6-BISPHOSPHATASE (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE) COMPLEXED WITH AMP, 2,5-ANHYDRO-D-GLUCITOL-1,6-BISPHOSPHATE AND POTASSIUM IONS (100 MM)
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER) / HYDROLASE / PHOSPHORIC MONOESTER / CARBOHYDRATE METABOLISM
Function / homology
Function and homology information


Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process ...Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,5-anhydro-1,6-di-O-phosphono-D-glucitol / ADENOSINE MONOPHOSPHATE / : / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsVilleret, V. / Lipscomb, W.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystallographic evidence for the action of potassium, thallium, and lithium ions on fructose-1,6-bisphosphatase.
Authors: Villeret, V. / Huang, S. / Fromm, H.J. / Lipscomb, W.N.
#1: Journal: Biochemistry / Year: 1995
Title: Structural Aspects of the Allosteric Inhibition of Fructose-1,6-Bisphosphatase by AMP: The Binding of Both the Substrate Analogue 2,5-Anhydro-D-Glucitol 1,6-Bisphosphate and Catalytic Metal ...Title: Structural Aspects of the Allosteric Inhibition of Fructose-1,6-Bisphosphatase by AMP: The Binding of Both the Substrate Analogue 2,5-Anhydro-D-Glucitol 1,6-Bisphosphate and Catalytic Metal Ions Monitored by X-Ray Crystallography
Authors: Villeret, V. / Huang, S. / Zhang, Y. / Lipscomb, W.N.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1993
Title: Structural Similarities between Fructose-1,6-Bisphosphatase and Inositol Monophosphatase
Authors: Zhang, Y. / Liang, J.Y. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1993
Title: Crystallographic Studies of the Catalytic Mechanism of the Neutral Form of Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.Y. / Huang, S. / Ke, H. / Lipscomb, W.N.
History
DepositionJun 2, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-1,6-BISPHOSPHATASE
B: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,58312
Polymers73,0062
Non-polymers1,57710
Water2,000111
1
A: FRUCTOSE-1,6-BISPHOSPHATASE
B: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE-1,6-BISPHOSPHATASE
B: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,16724
Polymers146,0124
Non-polymers3,15520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area23510 Å2
ΔGint-113 kcal/mol
Surface area41380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.200, 167.100, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHERE ARE TWO MONOMERS IN THE ASYMMETRIC UNIT, WHICH IS HALF THE MOLECULE. RESIDUES 1 - 8 AND 62 - 71 WERE OMITTED IN THE MODEL DUE TO A LACK OF WELL-DEFINED ELECTRON DENSITY.

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Components

#1: Protein FRUCTOSE-1,6-BISPHOSPHATASE / D-FRUCTOSE-1 / 6-BISPHOSPHATE 1-PHOSPHOHYDROLASE


Mass: 36503.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / References: UniProt: P00636, fructose-bisphosphatase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Sugar ChemComp-AHG / 2,5-anhydro-1,6-di-O-phosphono-D-glucitol / 2,5-ANHYDROGLUCITOL-1,6-BIPHOSPHATE


Type: D-saccharide / Mass: 324.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O11P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlenzyme11
220 mMTris base12
311-12.5 %PEG335012
45.0 mM12NaN3
51.0 mM2-mercaptoethanol12
60.1 mMmaleic acid12
71 mMAhG-1,6-P212
81 mMAMP12

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Date: Feb 27, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 31345 / % possible obs: 89 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. obs: 29101 / % possible obs: 83 % / Num. measured all: 98031

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.199 --
obs0.199 29101 84 %
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 90 111 5053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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