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- PDB-7tff: Crystal structure of human platelet phosphofructokinase-1 mutant-... -

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Basic information

Entry
Database: PDB / ID: 7tff
TitleCrystal structure of human platelet phosphofructokinase-1 mutant- D564N
ComponentsATP-dependent 6-phosphofructokinase, platelet type
KeywordsTRANSFERASE / Kinase / Somatic mutation
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, platelet type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHansen, H. / Webb, B.A. / Robart, A.R. / Narayanasami, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) United States
CitationJournal: Biochem.J. / Year: 2023
Title: Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity.
Authors: Voronkova, M.A. / Hansen, H.L. / Cooper, M.P. / Miller, J. / Sukumar, N. / Geldenhuys, W.J. / Robart, A.R. / Webb, B.A.
History
DepositionJan 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent 6-phosphofructokinase, platelet type
B: ATP-dependent 6-phosphofructokinase, platelet type
C: ATP-dependent 6-phosphofructokinase, platelet type
D: ATP-dependent 6-phosphofructokinase, platelet type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,58425
Polymers356,5754
Non-polymers2,00921
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17610 Å2
ΔGint-301 kcal/mol
Surface area103840 Å2
Unit cell
Length a, b, c (Å)77.889, 159.655, 131.248
Angle α, β, γ (deg.)90.000, 104.008, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
ATP-dependent 6-phosphofructokinase, platelet type / ATP-PFK / PFK-P / 6-phosphofructokinase type C / Phosphofructo-1-kinase isozyme C / PFK-C / Phosphohexokinase


Mass: 89143.742 Da / Num. of mol.: 4 / Mutation: D564N
Source method: isolated from a genetically manipulated source
Details: recombinant PFKP with His tag, mutation D564N / Source: (gene. exp.) Homo sapiens (human) / Gene: PFKP, PFKF / Plasmid: pFastBac HTa / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01813, 6-phosphofructokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 295.15 K / Method: microbatch / pH: 5.5
Details: 125uM ATP, 25% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→161.74 Å / Num. obs: 36675 / % possible obs: 98.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 127.22 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.132 / Rrim(I) all: 0.25 / Net I/σ(I): 6.2
Reflection shellResolution: 3.6→3.76 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4395 / Rpim(I) all: 0.742 / Rrim(I) all: 1.377 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XYK

4xyk


Resolution: 3.6→66.57 Å / SU ML: 0.6923 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3067 2001 5.56 %
Rwork0.2504 33989 -
obs0.2536 35990 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.05 Å2
Refinement stepCycle: LAST / Resolution: 3.6→66.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22403 0 105 64 22572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001122846
X-RAY DIFFRACTIONf_angle_d0.346530860
X-RAY DIFFRACTIONf_chiral_restr0.0393476
X-RAY DIFFRACTIONf_plane_restr0.00233993
X-RAY DIFFRACTIONf_dihedral_angle_d2.62093169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.39621450.34982410X-RAY DIFFRACTION98.57
3.69-3.790.35481500.33032413X-RAY DIFFRACTION99.73
3.79-3.90.38821310.3162441X-RAY DIFFRACTION99.69
3.9-4.030.36661380.30512400X-RAY DIFFRACTION99.65
4.03-4.170.33871440.29952408X-RAY DIFFRACTION99.77
4.17-4.340.351440.28092469X-RAY DIFFRACTION99.92
4.34-4.540.33991370.26632428X-RAY DIFFRACTION99.88
4.54-4.770.32581520.25012389X-RAY DIFFRACTION99.69
4.77-5.070.32181440.24432434X-RAY DIFFRACTION99.77
5.07-5.470.32251450.25882416X-RAY DIFFRACTION99.11
5.47-6.010.31931380.26792449X-RAY DIFFRACTION99.85
6.02-6.880.32121470.25532422X-RAY DIFFRACTION99.73
6.89-8.670.24521420.21312456X-RAY DIFFRACTION99.58
8.67-66.570.24621440.19212454X-RAY DIFFRACTION98.6

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