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- PDB-2jjk: FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSP... -

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Basic information

Entry
Database: PDB / ID: 2jjk
TitleFRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH A DUAL BINDING AMP SITE INHIBITOR
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE 1
KeywordsHYDROLASE / HYDROLASE (PHOSPHORIC MONOESTER) / DISEASE MUTATION / ALLOSTERIC ENZYME / ZINC / POLYMORPHISM / GLUCONEOGENESIS / CARBOHYDRATE METABOLISM
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / Gluconeogenesis / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / Gluconeogenesis / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / dephosphorylation / AMP binding / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / 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
Chem-R15 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRuf, A. / Joseph, C. / Benz, J. / Fol, B. / Tetaz, T. / Hebeisen, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Allosteric Fbpase Inhibitors Gain 10(5) Times in Potency When Simultaneously Binding Two Neighboring AMP Sites.
Authors: Hebeisen, P. / Kuhn, B. / Kohler, P. / Gubler, M. / Huber, W. / Kitas, E. / Schott, B. / Benz, J. / Joseph, C. / Ruf, A.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,5696
Polymers147,4384
Non-polymers1,1312
Water19,4921082
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19470 Å2
ΔGint-95.2 kcal/mol
Surface area54400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.176, 83.012, 277.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 500
2115B1 - 500
3115C1 - 500
4115D1 - 500
1124A1336
2124D1336

NCS ensembles :
ID
1
2

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Components

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


Mass: 36859.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: LIVER / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical ChemComp-R15 / N,N'-(heptane-1,7-diyldicarbamoyl)bis(3-chlorobenzenesulfonamide)


Mass: 565.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26Cl2N4O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsR15: BISULFONYLUREA

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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: 2.53 Å3/Da / Density % sol: 51.08 % / Description: NONE
Crystal growDetails: RESERVOIR = 0.1M HEPES PH7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 95035 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.5 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.88 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.385 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4767 5 %RANDOM
Rwork0.213 ---
obs0.216 90267 89.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9729 0 70 1082 10881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.99913488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94851263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82324.375384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.147151777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.751.56307
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.314210153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17533682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3634.53335
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1268medium positional0.30.5
12B1268medium positional0.360.5
13C1268medium positional0.330.5
14D1268medium positional0.350.5
21A42medium positional0.090.5
22D42medium positional0.090.5
11A1158loose positional0.595
12B1158loose positional0.715
13C1158loose positional0.715
14D1158loose positional0.715
11A1268medium thermal2.762
12B1268medium thermal1.612
13C1268medium thermal1.592
14D1268medium thermal2.32
21A42medium thermal0.732
22D42medium thermal0.732
11A1158loose thermal3.1510
12B1158loose thermal2.2510
13C1158loose thermal2.3910
14D1158loose thermal2.910
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 354
Rwork0.268 6720

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