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- PDB-3qpu: PFKFB3 in complex with PPi -

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Basic information

Entry
Database: PDB / ID: 3qpu
TitlePFKFB3 in complex with PPi
Components6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
KeywordsTRANSFERASE / HYDROLASE / kinase/bisphosphatase
Function / homology
Function and homology information


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 / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / fructose metabolic process / nucleoplasm / 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
PYROPHOSPHATE 2- / S,R MESO-TARTARIC ACID / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCavalier, M.C. / Kim, S.G. / Neau, D. / Lee, Y.H.
CitationJournal: Proteins / Year: 2012
Title: Molecular basis of the fructose-2,6-bisphosphatase reaction of PFKFB3: Transition state and the C-terminal function.
Authors: Cavalier, M.C. / Kim, S.G. / Neau, D. / Lee, Y.H.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6468
Polymers59,6941
Non-polymers9527
Water5,765320
1
A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
hetero molecules

A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,29316
Polymers119,3882
Non-polymers1,90414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)102.975, 102.975, 258.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

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Components

#1: Protein 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 / 6PF-2-K/Fru-2 / 6-P2ase 3 / PFK/FBPase 3 / 6PF-2-K/Fru-2 / 6-P2ase brain/placenta-type isozyme / ...6PF-2-K/Fru-2 / 6-P2ase 3 / PFK/FBPase 3 / 6PF-2-K/Fru-2 / 6-P2ase brain/placenta-type isozyme / Renal carcinoma antigen NY-REN-56 / iPFK-2 / 6-phosphofructo-2-kinase / Fructose-2 / 6-bisphosphatase


Mass: 59694.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKFB3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16875, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCl,20-25% ethylene glycol, 200-400mM Tartaric Acid, 5% glycerol, and 12% polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2009
RadiationMonochromator: silicon crystals (311 and 220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 34913 / Num. obs: 34913 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.34 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.039 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23594 1836 5 %RANDOM
Rwork0.18447 ---
all0.187 34913 --
obs0.187 34913 99.73 %-
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: 42.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 55 320 3951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9785012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21623.333183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97115665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051535
X-RAY DIFFRACTIONr_chiral_restr0.1390.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212794
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_it1.2731.52204
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39923588
X-RAY DIFFRACTIONr_scbond_it3.77831502
X-RAY DIFFRACTIONr_scangle_it6.0774.51423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 112 -
Rwork0.228 2523 -
obs--98.8 %
Refinement TLS params.Method: refined / Origin x: -20.5985 Å / Origin y: 60.4994 Å / Origin z: 8.9277 Å
111213212223313233
T0.053 Å20.0114 Å20.0029 Å2-0.0269 Å2-0.0136 Å2--0.0125 Å2
L0.8673 °2-0.1851 °2-0.137 °2-0.5826 °20.3227 °2--0.8867 °2
S0.0738 Å °0.0484 Å °-0.0677 Å °-0.1224 Å °-0.1007 Å °0.0263 Å °0.0221 Å °-0.0472 Å °0.0269 Å °

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