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- PDB-3o8o: Structure of phosphofructokinase from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3o8o
TitleStructure of phosphofructokinase from Saccharomyces cerevisiae
Components
  • 6-phosphofructokinase subunit alpha
  • 6-phosphofructokinase subunit beta
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase complex / Glycolysis / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / vacuolar acidification / canonical glycolysis ...vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase complex / Glycolysis / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / vacuolar acidification / canonical glycolysis / Neutrophil degranulation / proton transmembrane transport / glycolytic process / regulation of intracellular pH / mitochondrial outer membrane / mRNA binding / mitochondrion / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phosphofructokinase, N-terminal domain / Phosphofructokinase N-terminal domain yeast / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase ...Phosphofructokinase, N-terminal domain / Phosphofructokinase N-terminal domain yeast / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / 2,6-di-O-phosphono-beta-D-fructofuranose / ATP-dependent 6-phosphofructokinase subunit alpha / ATP-dependent 6-phosphofructokinase subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBanaszak, K. / Mechin, I. / Kopperschlager, G. / Rypniewski, W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle.
Authors: Banaszak, K. / Mechin, I. / Obmolova, G. / Oldham, M. / Chang, S.H. / Ruiz, T. / Radermacher, M. / Kopperschlager, G. / Rypniewski, W.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphofructokinase subunit alpha
B: 6-phosphofructokinase subunit beta
C: 6-phosphofructokinase subunit alpha
D: 6-phosphofructokinase subunit beta
E: 6-phosphofructokinase subunit alpha
F: 6-phosphofructokinase subunit beta
G: 6-phosphofructokinase subunit alpha
H: 6-phosphofructokinase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)682,96324
Polymers678,1618
Non-polymers4,80216
Water00
1
A: 6-phosphofructokinase subunit alpha
B: 6-phosphofructokinase subunit beta
C: 6-phosphofructokinase subunit alpha
D: 6-phosphofructokinase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,48112
Polymers339,0804
Non-polymers2,4018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-46 kcal/mol
Surface area100230 Å2
MethodPISA
2
E: 6-phosphofructokinase subunit alpha
F: 6-phosphofructokinase subunit beta
G: 6-phosphofructokinase subunit alpha
H: 6-phosphofructokinase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,48112
Polymers339,0804
Non-polymers2,4018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16420 Å2
ΔGint-53 kcal/mol
Surface area100860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.046, 186.205, 236.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
6-phosphofructokinase subunit alpha / Phosphofructokinase 1 / Phosphohexokinase / 6PF-1-K subunit alpha


Mass: 86002.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PFK1, YGR240C, G8599 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PS1 / References: UniProt: P16861, 6-phosphofructokinase
#2: Protein
6-phosphofructokinase subunit beta / Phosphofructokinase 2 / Phosphohexokinase / 6PF-1-K subunit beta


Mass: 83537.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PFK2, YMR205C, YM8325.06C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PS1 / References: UniProt: P16862, 6-phosphofructokinase
#3: 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Sugar
ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6-10% PEG4000, 0.2 mM sodium acetate, 0.1 M MES buffer pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1044 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 1997
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1044 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. all: 172818 / Num. obs: 172818 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.075 / Net I/σ(I): 15.13
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.75 / Rsym value: 0.557 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PFK

1pfk


Resolution: 2.9→35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3092 3446 random
Rwork0.2586 --
obs0.2586 172763 -
all-172763 -
Refinement stepCycle: LAST / Resolution: 2.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46357 0 288 0 46645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011291
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.61924
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3f6p_xplor.par
X-RAY DIFFRACTION4fdp.param

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