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- PDB-1q9d: Fructose-1,6-bisphosphatase Complexed with a New Allosteric Site ... -

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Basic information

Entry
Database: PDB / ID: 1q9d
TitleFructose-1,6-bisphosphatase Complexed with a New Allosteric Site Inhibitor (I-State)
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE / BISPHOSPHATASE
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
6-O-phosphono-beta-D-fructofuranose / Chem-OI1 / PHOSPHATE ION / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHonzatko, R.B. / Choe, J.Y.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors
Authors: Choe, J.Y. / Nelson, S.W. / Arienti, K.L. / Axe, F.U. / Collins, T.L. / Jones, T.K. / Kimmich, R.D. / Newman, M.J. / Norvell, K. / Ripka, W.C. / Romano, S.J. / Short, K.M. / Slee, D.H. / ...Authors: Choe, J.Y. / Nelson, S.W. / Arienti, K.L. / Axe, F.U. / Collins, T.L. / Jones, T.K. / Kimmich, R.D. / Newman, M.J. / Norvell, K. / Ripka, W.C. / Romano, S.J. / Short, K.M. / Slee, D.H. / Fromm, H.J. / Honzatko, R.B.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)75,46314
Polymers73,3822
Non-polymers2,08112
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-110 kcal/mol
Surface area26320 Å2
MethodPISA
2
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)150,92628
Polymers146,7654
Non-polymers4,16124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area24790 Å2
ΔGint-242 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.860, 166.250, 80.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Fructose-1,6-bisphosphatase / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase / FBPase


Mass: 36691.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: liver / Production host: Escherichia coli (E. coli) / Strain (production host): DF657 / References: UniProt: P00636, fructose-bisphosphatase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 301 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-OI1 / 3-(4-HYDROXYBENZYL)-2-[1-({[2-(4-HYDROXYPHENYL)ETHYL]AMINO}CARBONYL)BUTYL]-4-OXO-3,6,11,11A-TETRAHYDRO-4H-PYRAZINO[1,2-B]ISOQUINOLIN-2-IUM-1-OLATE


Mass: 541.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H35N3O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.58 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, Tris-malonate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMKPi1droppH7.4
35 mM1dropMgCl2
45 mMF6P1drop
52 mMOC2521drop
62.5 mMTris malonate1reservoirpH7.4
76 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 16, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 32966 / Num. obs: 28849 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.35→2.45 Å / % possible all: 66
Reflection
*PLUS
Num. measured all: 94949
Reflection shell
*PLUS
Lowest resolution: 2.44 Å / % possible obs: 65.5 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYJ

1eyj


Resolution: 2.35→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 2716 RANDOM
Rwork0.191 --
all0.197 27163 -
obs0.197 27163 -
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 136 291 5433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d5.74
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg5.74

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