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- PDB-2vt5: FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSP... -

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Basic information

Entry
Database: PDB / ID: 2vt5
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-ROK / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRuf, A. / Joseph, C. / Benz, J. / Fol, B. / Tetaz, T.
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
DepositionMay 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,07816
Polymers294,8758
Non-polymers2,2038
Water9,692538
1
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)148,5398
Polymers147,4384
Non-polymers1,1014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-109.8 kcal/mol
Surface area54280 Å2
MethodPQS
2
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5398
Polymers147,4384
Non-polymers1,1014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18520 Å2
ΔGint-85.8 kcal/mol
Surface area53830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.964, 284.611, 83.375
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C
14D
15E
16F
17G
18H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 500
1125B1 - 500
1135C1 - 500
1145D1 - 500
1155E1 - 500
1165F1 - 500
1175G1 - 500
1185H1 - 500

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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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.: 8
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-ROK / 4-AMINO-N-[(2-SULFANYLETHYL)CARBAMOYL]BENZENESULFONAMIDE


Mass: 275.348 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H13N3O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsROK: THE INHIBITOR MOLECULES FORM DISULFIDE DIMERS N,N'-[DITHIOBIS(ETHANE-2,1-DIYLIMINOCARBONYL)] ...ROK: THE INHIBITOR MOLECULES FORM DISULFIDE DIMERS N,N'-[DITHIOBIS(ETHANE-2,1-DIYLIMINOCARBONYL)] BIS(4-AMINOBENZENESULFONAMIDE) ACROSS SUBUNIT INTERFACES A-C, B-D, E-G, AND F-H.

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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: 2.75 Å3/Da / Density % sol: 54.94 % / 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: 0.984
DetectorType: MARRESEARCH / Detector: CCD / Date: May 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 406033 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.3 / % possible all: 46

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.956 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ALLOSTERIC INHIBITORS FORM DISULFIDE DIMERS ACROSS THE AMP-SITES OF FBPASE MONOMERS A AND C, B AND D, E AND G, AND F AND H.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 6862 5 %RANDOM
Rwork0.203 ---
obs0.205 129505 88.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0.22 Å2
2---0.23 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19440 0 136 538 20114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02219957
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.99726953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93852524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89124.264774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.802153561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.93715102
X-RAY DIFFRACTIONr_chiral_restr0.0850.23062
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.29829
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.213747
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.21065
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_other0.1770.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.512970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.127220293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64237895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5574.56660
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

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1268medium positional0.260.5
B1268medium positional0.250.5
C1268medium positional0.40.5
D1268medium positional0.270.5
E1268medium positional0.190.5
F1268medium positional0.230.5
G1268medium positional0.410.5
H1268medium positional0.250.5
A1169loose positional0.725
B1169loose positional0.815
C1169loose positional0.875
D1169loose positional0.795
E1169loose positional1.415
F1169loose positional0.835
G1169loose positional1.495
H1169loose positional0.875
A1268medium thermal0.642
B1268medium thermal1.012
C1268medium thermal0.922
D1268medium thermal1.262
E1268medium thermal1.442
F1268medium thermal1.042
G1268medium thermal0.922
H1268medium thermal12
A1169loose thermal1.5510
B1169loose thermal1.9610
C1169loose thermal2.0910
D1169loose thermal2.3210
E1169loose thermal2.4810
F1169loose thermal210
G1169loose thermal2.1410
H1169loose thermal2.110
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.396 285
Rwork0.29 5184

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