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- PDB-1lev: PORCINE KIDNEY FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH AN AMP-... -

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Basic information

Entry
Database: PDB / ID: 1lev
TitlePORCINE KIDNEY FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH AN AMP-SITE INHIBITOR
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE
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
Chem-CLI / 6-O-phosphono-beta-D-fructofuranose / : / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWright, S.W. / Carlo, A.A. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Mansour, M.N. / McClure, L.D. / Pandit, J. / Schulte, G.K. / Treadway, J.L. ...Wright, S.W. / Carlo, A.A. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Mansour, M.N. / McClure, L.D. / Pandit, J. / Schulte, G.K. / Treadway, J.L. / Wang, I.-K. / Bauer, P.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: 3-(2-carboxyethyl)-4,6-dichloro-1H-indole-2-carboxylic acid: an allosteric inhibitor of fructose-1,6-bisphosphatase at the AMP site.
Authors: Wright, S.W. / Carlo, A.A. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Mansour, M.N. / McClure, L.D. / Pandit, J. / Schulte, G.K. / Treadway, J.L. / Wang, I.-K. / Bauer, P.H.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_residues
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase
F: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75510
Polymers73,4102
Non-polymers1,3448
Water1,910106
1
A: Fructose-1,6-bisphosphatase
F: Fructose-1,6-bisphosphatase
hetero molecules

A: Fructose-1,6-bisphosphatase
F: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,50920
Polymers146,8214
Non-polymers2,68816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18030 Å2
ΔGint-171 kcal/mol
Surface area42690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.870, 73.446, 78.025
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x, y, -z.

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Components

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


Mass: 36705.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / 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
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CLI / 3-(2-CARBOXY-ETHYL)-4,6-DICHLORO-1H-INDOLE-2-CARBOXYLIC ACID / MDL-29951


Mass: 302.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9Cl2NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Na Acetate, 13.75% PEG 4000, 0.1M Hepes pH7.0, 1mM F6P, 2mM MnCl2, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 Mpotassium phosphate1droppH7.2
21 mMEDTA1drop
31 mMbeta-mercaptoethanol1drop
42.0 mM1dropMnCl2
51 mMcompound 11drop
615 mg/mlprotein1drop
72 mMfructose6-phosphate1drop
8100 mMHEPES1reservoirpH7.0
9200 mMsodium acetate1reservoir
1013.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 23, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40.26 Å / Num. obs: 32736 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.44 / Num. unique all: 2255 / % possible all: 64.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FBP

1fbp


Resolution: 2.15→40.26 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.169 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25514 1639 5 %RANDOM
Rwork0.19269 ---
all0.19582 32734 --
obs0.19582 32734 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-1.12 Å2
2---0.13 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 74 106 4947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224919
X-RAY DIFFRACTIONr_bond_other_d0.0030.024567
X-RAY DIFFRACTIONr_angle_refined_deg3.041.9956662
X-RAY DIFFRACTIONr_angle_other_deg1.661310657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0563618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.57315930
X-RAY DIFFRACTIONr_chiral_restr0.1680.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025359
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02915
X-RAY DIFFRACTIONr_nbd_refined0.2440.31153
X-RAY DIFFRACTIONr_nbd_other0.250.34676
X-RAY DIFFRACTIONr_nbtor_other0.1060.55
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.5343
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4220.390
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.491.53087
X-RAY DIFFRACTIONr_mcangle_it4.29524988
X-RAY DIFFRACTIONr_scbond_it4.89431832
X-RAY DIFFRACTIONr_scangle_it7.0594.51674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 81
Rwork0.226 1464
Refinement
*PLUS
Rfactor Rfree: 0.283 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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