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- PDB-3fbp: STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCT... -

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Basic information

Entry
Database: PDB / ID: 3fbp
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 / sucrose biosynthetic process / 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 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding ...Gluconeogenesis / sucrose biosynthetic process / 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 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / 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 / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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 class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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
2,6-di-O-phosphono-beta-D-fructofuranose / 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 25, 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 21, 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)73,6864
Polymers73,0062
Non-polymers6802
Water0
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)147,3728
Polymers146,0124
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16100 Å2
ΔGint-80 kcal/mol
Surface area44250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.600, 131.600, 68.900
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: (-0.24308, -0.41623, -0.87616), (-0.42065, -0.76867, 0.48187), (-0.87416, 0.48575, 0.01177)
Vector: 87.1615, 154.86459, 1.58597)
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
#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 / Fructose 2,6-bisphosphate


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal grow
*PLUS
pH: 7.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlenzyme11
210 mMTris base12
38 %(w/v)PEG335012
40.1 mMEDTA12
50.3 mM12NaN3
62.5 mMmaleic acid12

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 15546 / % possible obs: 95 % / Num. measured all: 61118 / Rmerge(I) obs: 0.063

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.188 / 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. atoms4858 0 40 0 4898
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: 0.188 / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg4

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