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- PDB-9qv2: 1-Phosphofructokinase mutant K95H from E. coli with bound fructos... -

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Basic information

Entry
Database: PDB / ID: 9qv2
Title1-Phosphofructokinase mutant K95H from E. coli with bound fructose 6-phosphate and ADP
Components1-phosphofructokinase
KeywordsTRANSFERASE / fructose / fructose-1-phosphate / fructose-6-phosphate / kinase / FruK / ATP / ADP / 1-phosphofructokinase
Function / homology
Function and homology information


1-phosphofructokinase / 1-phosphofructokinase activity / fructose catabolic process / phosphofructokinase activity / ATP binding / cytosol
Similarity search - Function
Fructose 1-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / : / : / 1-phosphofructokinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZarzycki, J. / Dronsella, B. / Erb, T.J. / Lindner, S.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Federal Ministry for Education and Research033RC023G Germany
CitationJournal: To Be Published
Title: Structural investigation of gain of function mutations in 1-phosphofructokinase (FruK) of E. coli
Authors: Dronsella, B. / Zarzycki, J. / Satanowski, A. / Bar-Even, A. / Erb, T.J. / Lindner, S.N.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6487
Polymers33,7991
Non-polymers8506
Water5,621312
1
A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules


  • defined by author
  • Evidence: gel filtration, In gel filtration experiments and during purifaction FruK eluted as a tetramer. However, according to PDBePISA only a homodimer should be stable. Note, that FruK was ...Evidence: gel filtration, In gel filtration experiments and during purifaction FruK eluted as a tetramer. However, according to PDBePISA only a homodimer should be stable. Note, that FruK was crystallized in the presence of substrates/products.
  • 139 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)138,59328
Polymers135,1944
Non-polymers3,39924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)63.560, 99.080, 140.620
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 1-phosphofructokinase / Fructose 1-phosphate kinase / Fru1PK


Mass: 33798.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fruK, fpk, b2168, JW2155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEW9, 1-phosphofructokinase
#4: 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: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 317 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.28 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: The FruK variant K95H (3.4 mg/mL) in 20 mM MOPS/KOH buffer (pH 7.4) containing 75 mM KCl and 1 M L-proline was mixed in a 1:1 ratio with condition containing 1 M ammonium sulfate, 75 mM ...Details: The FruK variant K95H (3.4 mg/mL) in 20 mM MOPS/KOH buffer (pH 7.4) containing 75 mM KCl and 1 M L-proline was mixed in a 1:1 ratio with condition containing 1 M ammonium sulfate, 75 mM TRIS/HCl (pH 8.5), 150 mM lithium sulfate, 8 mM fructose-6-phosphate, 4 mM ADP, and 10 mM magnesium chloride. The final drop volume was 0.8 microliters. Before plunge freezing in liquid nitrogen, the crystals were soaked with additional 25 mM fructose-6-phosphate, 12.5 mM magnesium chloride for about 1 minute, before glycerol was added as a cryo-protectant to a final concentration of 30% (v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.85→29.38 Å / Num. obs: 38279 / % possible obs: 99.9 % / Redundancy: 7.59 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Net I/σ(I): 17.09
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.85-1.90.64128090.9030.6881
1.9-1.950.52927360.9240.5681
1.95-2.010.36726540.9570.3941
2.01-2.070.30525680.9650.3271
2.07-2.140.25924970.9740.2781
2.14-2.210.20724310.9810.2221
2.21-2.290.17523470.9860.1881
2.29-2.390.15622290.9880.1671
2.39-2.490.13121790.9910.141
2.49-2.620.10720920.9930.1151
2.62-2.760.09219540.9960.0991
2.76-2.930.07718840.9960.0821
2.93-3.130.06417580.9970.0681
3.13-3.380.05416530.9980.0591
3.38-3.70.04515280.9980.0491
3.7-4.140.04313830.9980.0461
4.14-4.780.03812270.9990.0411
4.78-5.850.03810590.9980.0411
5.85-8.270.0388310.9990.0411
8.27-29.380.0314600.9990.0341

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.38 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 2000 5.23 %
Rwork0.1588 --
obs0.1604 38271 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 52 312 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192461
X-RAY DIFFRACTIONf_angle_d1.323352
X-RAY DIFFRACTIONf_dihedral_angle_d22.962906
X-RAY DIFFRACTIONf_chiral_restr0.112388
X-RAY DIFFRACTIONf_plane_restr0.015427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.25781420.23522559X-RAY DIFFRACTION100
1.9-1.950.23571420.19622578X-RAY DIFFRACTION100
1.95-20.22051410.17272558X-RAY DIFFRACTION100
2-2.070.17681400.16432547X-RAY DIFFRACTION100
2.07-2.140.21451410.15562568X-RAY DIFFRACTION100
2.14-2.230.21151420.1612571X-RAY DIFFRACTION100
2.23-2.330.20371420.16382569X-RAY DIFFRACTION100
2.33-2.450.18171410.16092567X-RAY DIFFRACTION100
2.45-2.610.19061430.15332594X-RAY DIFFRACTION100
2.61-2.810.17841420.15932575X-RAY DIFFRACTION100
2.81-3.090.16451440.16222603X-RAY DIFFRACTION100
3.09-3.540.18641440.15232625X-RAY DIFFRACTION100
3.54-4.450.17541440.14342621X-RAY DIFFRACTION100
4.45-29.380.18811520.15432736X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.2006 Å / Origin y: 20.5227 Å / Origin z: 49.8853 Å
111213212223313233
T0.1093 Å2-0.0134 Å2-0.0114 Å2-0.1314 Å20.0287 Å2--0.1409 Å2
L0.9891 °2-0.2001 °20.1085 °2-1.0887 °2-0.4793 °2--1.4609 °2
S-0.0483 Å °0.0958 Å °0.1591 Å °0.0178 Å °0.0199 Å °0.0064 Å °-0.0824 Å °0.0302 Å °0.0033 Å °
Refinement TLS groupSelection details: all

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