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- PDB-1frp: CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH F... -

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Basic information

Entry
Database: PDB / ID: 1frp
TitleCRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH FRUCTOSE-2,6-BISPHOSPHATE, AMP AND ZN2+ AT 2.0 ANGSTROMS RESOLUTION. ASPECTS OF SYNERGISM BETWEEN INHIBITORS
ComponentsFRUCTOSE 1,6-BISPHOSPHATASE
KeywordsHYDROLASE(PHOSPHORIC MONOESTER)
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
ADENOSINE MONOPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructofuranose / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsXue, Y. / Huang, S. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of fructose-1,6-bisphosphatase complexed with fructose 2,6-bisphosphate, AMP, and Zn2+ at 2.0-A resolution: aspects of synergism between inhibitors.
Authors: Xue, Y. / Huang, S. / Liang, J.Y. / Zhang, Y. / Lipscomb, W.N.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal Structure of the Neutral Form of Fructose 1,6-Bisphosphatase Complexed with Regulatory Inhibitor Fructose 2,6-Bisphosphate at 2.6 Angstroms Resolution
Authors: Liang, J.-Y. / Huang, S. / Zhang, Y. / Ke, H. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1991
Title: Conformational Transition of Fructose 1,6-Bisphosphatase: Structure Comparison between the AMP Complex (T Form) and the Fructose 6-Phosphate Complex (R Form)
Authors: Ke, H. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N.
History
DepositionAug 26, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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

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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)74,4798
Polymers72,9742
Non-polymers1,5056
Water4,306239
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)148,95916
Polymers145,9484
Non-polymers3,01112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area21300 Å2
ΔGint-271 kcal/mol
Surface area42010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.950, 166.300, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein FRUCTOSE 1,6-BISPHOSPHATASE


Mass: 36487.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00636, fructose-bisphosphatase
#2: Sugar ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growpH: 7.4 / Details: pH 7.4, ROOM TEMPERATURE, COCRYSTALLIZATION.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-17 mg/mlprotein11
220 mMTris-HCl12
31.0 mMAMP12
40.2 mMFru-2,6-P212
50.006 mM12ZnCl2
65 mM12NaN3
71 mM2-mercaptoethanol12
80.1 mMEDTA12
915 %(w/v)PEG335012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 49540 / % possible obs: 82.8 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. measured all: 115147 / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 45437
Displacement parametersBiso mean: 30.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 88 239 5223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.8
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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