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- PDB-2fbp: STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCT... -

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Basic information

Entry
Database: PDB / ID: 2fbp
TitleSTRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION
ComponentsFRUCTOSE 1,6-BISPHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER)
Function / homology
Function and homology information


Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process ...Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / dephosphorylation / 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 / cytosol / cytoplasm
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
Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKe, H. / Thorpe, C.M. / Seaton, B.A. / Marcus, F. / Lipscomb, W.N.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structure refinement of fructose-1,6-bisphosphatase and its fructose 2,6-bisphosphate complex at 2.8 A resolution.
Authors: Ke, H.M. / Thorpe, C.M. / Seaton, B. / Lipscomb, W.N. / Marcus, F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal Structure of the Neutral Form of Fructose-1,6-Bisphosphatase Complexed with the Product Fructose 6-Phosphate at 2.1-Angstroms Resolution
Authors: Ke, H. / Zhang, Y. / Liang, J.-Y. / Lipscomb, W.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Crystal Structure of Fructose-1,6-Bisphosphatase Complexed with Fructose 6-Phosphate, AMP, and Magnesium
Authors: Ke, H. / Zhang, Y. / Lipscomb, W.N.
History
DepositionJun 7, 1990Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)73,0062
Polymers73,0062
Non-polymers00
Water00
1
A: FRUCTOSE 1,6-BISPHOSPHATASE
B: FRUCTOSE 1,6-BISPHOSPHATASE

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


Theoretical massNumber of molelcules
Total (without water)146,0124
Polymers146,0124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13460 Å2
ΔGint-82 kcal/mol
Surface area45860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.300, 132.300, 68.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUES PRO A 147, AND PRO B 147 ARE CIS PROLINES. ALSO SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.23275, -0.41329, -0.88035), (-0.42999, -0.7682, 0.47432), (-0.87221, 0.48889, 0.00108)
Vector: 86.95872, 156.37512, 1.22618)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein FRUCTOSE 1,6-BISPHOSPHATASE


Mass: 36503.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00636, fructose-bisphosphatase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal grow
*PLUS
pH: 7.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlenzyme11
220 mMTris base12
32.5 mMmaleic acid12
40.1 mMEDTA12
50.3 mM12NaN3
64 %(w/v)PEG335012

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 16082 / % possible obs: 98 % / Num. measured all: 82889 / Rmerge(I) obs: 0.0598

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.194 / Highest resolution: 2.8 Å
Details: PRO A 147 AND PRO B 147 HAS BEEN REFINED TO A TRANS CONFORMATION IN THE NEWLY REFINED 2.1 ANGSTROM STRUCTURE OF F6P COMPLEX (H. KE, Y.ZHANG, J.-Y. LIANG, AND W. N. LIPSCOMB (1991) PROC. NATL. ...Details: PRO A 147 AND PRO B 147 HAS BEEN REFINED TO A TRANS CONFORMATION IN THE NEWLY REFINED 2.1 ANGSTROM STRUCTURE OF F6P COMPLEX (H. KE, Y.ZHANG, J.-Y. LIANG, AND W. N. LIPSCOMB (1991) PROC. NATL. ACAD. SCI. 88, 2989-2993).
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 0 0 4860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg4
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
Software
*PLUS
Name: XPLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.194 / Lowest resolution: 10 Å / Num. reflection obs: 15079
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_deg4

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