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- PDB-9qv0: 1-Phosphofructokinase (FruK) from E. coli with bound fructose 1-p... -

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Basic information

Entry
Database: PDB / ID: 9qv0
Title1-Phosphofructokinase (FruK) from E. coli with bound fructose 1-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 / 1-O-phosphono-beta-D-fructofuranose / : / : / 1-phosphofructokinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)34,8249
Polymers33,7901
Non-polymers1,0348
Water4,738263
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)139,29436
Polymers135,1584
Non-polymers4,13632
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)63.150, 98.460, 140.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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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: 33789.602 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
#3: Sugar ChemComp-F1X / 1-O-phosphono-beta-D-fructofuranose / beta D-Fructose 1-phosphate / 1-O-phosphono-beta-D-fructose / 1-O-phosphono-D-fructose / 1-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

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Non-polymers , 6 types, 270 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: FruK (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), ...Details: FruK (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, 2 mM fructose-1-phosphate, 4 mM ADP, and 10 mM magnesium chloride. The final drop volume was 0.8 microliters. Before plunge freezing the crystals in liquid nitrogen, glycerol was added to the drop as a cryo-protectant to a final concentration of 35% (v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→19.76 Å / Num. obs: 62272 / % possible obs: 97.5 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Net I/σ(I): 22.46
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.55-1.591.1232.545010.831.1991
1.59-1.630.85544670.8870.9061
1.63-1.680.82343220.8920.8731
1.68-1.730.88842320.9140.9421
1.73-1.790.61741200.9370.6571
1.79-1.850.46239400.9570.4911
1.85-1.920.30237580.9850.321
1.92-20.23235930.990.2471
2-2.090.17235050.9920.1841
2.09-2.190.12533200.9950.1331
2.19-2.310.09731840.9970.1031
2.31-2.450.07730550.9980.0821
2.45-2.620.05829130.9980.0621
2.62-2.830.04627130.9980.051
2.83-3.10.03725350.9990.0391
3.1-3.470.03122640.9990.0331
3.47-40.02919960.9990.0311
4-4.90.02417230.9990.0251
4.9-6.930.024136610.0251
6.93-19.760.0237650.9990.0241

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.76 Å / SU ML: 0.141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 2000 3.21 %
Rwork0.1708 60270 -
obs0.1711 62270 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 64 263 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572470
X-RAY DIFFRACTIONf_angle_d0.77393357
X-RAY DIFFRACTIONf_chiral_restr0.0549389
X-RAY DIFFRACTIONf_plane_restr0.0067426
X-RAY DIFFRACTIONf_dihedral_angle_d13.1142911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.25441390.23894182X-RAY DIFFRACTION96.26
1.59-1.630.24151420.21754281X-RAY DIFFRACTION97.98
1.63-1.680.22411410.20654269X-RAY DIFFRACTION98.28
1.68-1.730.23931430.20084294X-RAY DIFFRACTION98.14
1.73-1.80.2171430.20144312X-RAY DIFFRACTION98.24
1.8-1.870.21481410.19354252X-RAY DIFFRACTION97.08
1.87-1.950.21531400.18714215X-RAY DIFFRACTION96.07
1.95-2.060.21341390.1914207X-RAY DIFFRACTION96.15
2.06-2.180.17011410.17644230X-RAY DIFFRACTION96.26
2.18-2.350.18921420.17414288X-RAY DIFFRACTION97.04
2.35-2.590.18471440.17054328X-RAY DIFFRACTION98.31
2.59-2.960.16841470.1644432X-RAY DIFFRACTION99.37
2.96-3.730.15971460.15554388X-RAY DIFFRACTION98.16
3.73-19.760.1561520.15414592X-RAY DIFFRACTION98.83
Refinement TLS params.Method: refined / Origin x: 31.9602347979 Å / Origin y: 20.3756255048 Å / Origin z: 49.8708909068 Å
111213212223313233
T0.126585669546 Å2-0.0166462148511 Å2-0.00749726293992 Å2-0.125428140098 Å20.0204425967891 Å2--0.141775377504 Å2
L0.960713134508 °2-0.258422821284 °20.119303812273 °2-0.915717747552 °2-0.491793171639 °2--1.53935626434 °2
S-0.034365513192 Å °0.0790580526914 Å °0.122466769739 Å °-0.0159150343031 Å °0.031513608958 Å °0.00771597209533 Å °-0.0851686841456 Å °-0.00923466883515 Å °-0.00994351725948 Å °
Refinement TLS groupSelection details: all

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