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- PDB-1nv2: Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Ph... -

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Basic information

Entry
Database: PDB / ID: 1nv2
TitleFructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Phosphate, Phosphate and Thallium (20 mM)
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE / Bisphosphatase / Allosteric enzymes / Gluconeogenesis
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 / HYDROGENPHOSPHATE ION / PHOSPHATE ION / THALLIUM (I) ION / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChoe, J. / Iancu, C.V. / Fromm, H.J. / Honzatko, R.B.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Interaction of Tl+ with product complexes of fructose-1,6-bisphosphatase
Authors: Choe, J.Y. / Nelson, S.W. / Fromm, H.J. / Honzatko, R.B.
History
DepositionFeb 1, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,41712
Polymers36,6911
Non-polymers1,72611
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fructose-1,6-bisphosphatase
hetero molecules

A: Fructose-1,6-bisphosphatase
hetero molecules

A: Fructose-1,6-bisphosphatase
hetero molecules

A: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,66948
Polymers146,7654
Non-polymers6,90444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area21860 Å2
ΔGint-381 kcal/mol
Surface area44210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.361, 82.765, 165.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fructose-1,6-bisphosphatase


Mass: 36691.207 Da / Num. of mol.: 1
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.: 1
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 , 5 types, 236 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO4P
#6: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMG A2341 AND TL A2342 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. MG A2343 AND TL A2344 ARE IN ...MG A2341 AND TL A2342 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. MG A2343 AND TL A2344 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER

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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: 2.3 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
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
520 mMthalium acetate1drop
6100 mMHEPES1reservoirpH7.0
75 %t-butyl alcohol1reservoir
827 %(v/v)glycerol1reservoir
98 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: BRANDEIS / Detector: CCD / Date: May 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17604 / Num. obs: 17604 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.03
Reflection shellResolution: 2.1→2.19 Å / % possible all: 43.7
Reflection
*PLUS
Num. measured all: 92869
Reflection shell
*PLUS
% possible obs: 43.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYI

1eyi


Resolution: 2.1→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 1486 RANDOM
Rwork0.17 --
all0.178 14868 -
obs0.178 14868 -
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 34 226 2785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.28
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15652 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2487 / Rfactor Rwork: 0.1703
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg24.9
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.28

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