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- PDB-3bif: 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2... -

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Basic information

Entry
Database: PDB / ID: 3bif
Title6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2K ACTIVE SITE
ComponentsPROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE)
KeywordsTRANSFERASE / KINASE / PHOSPHOTRANSFERASE / PHOSPHATASE / HYDROLASE (PHOSPHO) / GLYCOLYSIS / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose metabolic process / ATP binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / SUCCINIC ACID / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuen, M.H. / Hasemann, C.A.
Citation
Journal: Biochemistry / Year: 1999
Title: A switch in the kinase domain of rat testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.
Authors: Yuen, M.H. / Wang, X.L. / Mizuguchi, H. / Uyeda, K. / Hasemann, C.A.
#1: Journal: Structure / Year: 1996
Title: The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies.
Authors: Hasemann, C.A. / Istvan, E.S. / Uyeda, K. / Deisenhofer, J.
History
DepositionMay 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8306
Polymers53,9371
Non-polymers8935
Water3,369187
1
A: PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66012
Polymers107,8752
Non-polymers1,78610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Unit cell
Length a, b, c (Å)106.700, 108.700, 71.700
Angle α, β, γ (deg.)90.00, 129.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE)


Mass: 53937.387 Da / Num. of mol.: 1 / Mutation: W15F, W64F, W299F, W320F
Source method: isolated from a genetically manipulated source
Details: BIFUNCTIONAL ENZYME, ALSO EC 3.1.3.46 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Gene: RT2K / Organ: TESTIS / Plasmid: PT7-7 / Cell line (production host): BL21 / Gene (production host): RT2K / Production host: Escherichia coli (E. coli) / Keywords: BIFUNCTIONAL ENZYME, ALSO EC 3.1.3.46 / References: UniProt: P25114, 6-phosphofructo-2-kinase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / BUTANEDIOIC ACID


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.97 Å3/Da / Density % sol: 57.6 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 50MM SUCCINATE, PH 5.5, 50MM TRIS-PO4, PH 7.5, 11% PEG 4000, 100UM EDTA, 10MM DTT, 10% GLYCEROL, 3MM MGCL2., pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlRT2K-Wo1drop
250 mMTris-PO41drop
35 %glycerol1drop
40.100 mMEDTA1drop
510 mMdithiothreitol1drop
60.5 %octyl beta-D-glucopyranoside1drop
73 mMF6P1drop
81 mMAMP-PNP1drop
911 %PEG40001reservoir
1050 mMsuccinate1reservoir
1150 mMTris-PO41reservoir
120.100 mMEDTA1reservoir
1310 mMdithiothreitol1reservoir
1410 %glycerol1reservoir
153 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 9, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23883 / % possible obs: 88.1 % / Observed criterion σ(I): 1 / Redundancy: 2.64 % / Biso Wilson estimate: 39.9 Å2 / Rsym value: 0.039 / Net I/σ(I): 36.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.16 / Rsym value: 0.15 / % possible all: 84.9
Reflection
*PLUS
Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 84.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BIF

1bif


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.0049 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / σ(F): 1
Details: THE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN SEQUENCE ANALYSIS OF A REDISSOLVED CRYSTAL CONFIRMED THE PRESENCE OF THE N-TERMINUS IN THE ...Details: THE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN SEQUENCE ANALYSIS OF A REDISSOLVED CRYSTAL CONFIRMED THE PRESENCE OF THE N-TERMINUS IN THE CRYSTALS. THE CONCLUSION IS THAT THE N-TERMINAL 36 AMINO ACIDS ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2434 10 %RANDOM
Rwork0.197 ---
obs-23883 85.2 %-
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 58 187 3764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.87
X-RAY DIFFRACTIONx_mcangle_it5.32
X-RAY DIFFRACTIONx_scbond_it5.48
X-RAY DIFFRACTIONx_scangle_it7.39
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.358 276 10 %
Rwork0.319 2457 -
obs--78.9 %
Xplor fileSerial no: 1 / Param file: ENGH & HUBER / Topol file: ENGH & HUBER
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 1 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 10 % / Rfactor Rwork: 0.319

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