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- PDB-9qv1: 1-Phosphofructokinase mutant K95H from E. coli with bound fructos... -

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Basic information

Entry
Database: PDB / ID: 9qv1
Title1-Phosphofructokinase mutant K95H 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: 1.54 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)34,6327
Polymers33,7991
Non-polymers8346
Water4,107228
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)138,52928
Polymers135,1944
Non-polymers3,33524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)62.980, 98.120, 139.850
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: 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
#6: 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, 233 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
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
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 the crystals in liquid nitrogen, glycerol was added to the drop 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: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.54→19.7 Å / Num. obs: 64212 / % possible obs: 99.8 % / Redundancy: 6.27 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.07 / Net I/σ(I): 15.11
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.54-1.580.50247150.9010.5541
1.58-1.620.4345820.9410.4681
1.62-1.670.35244580.9550.3831
1.67-1.720.28443650.9690.3091
1.72-1.780.23241890.9730.2541
1.78-1.840.17640570.9850.1921
1.84-1.910.13839510.9910.151
1.91-1.990.11337800.9930.1231
1.99-2.080.09936230.9930.1091
2.08-2.180.08434680.9940.0921
2.18-2.30.07332940.9950.0791
2.3-2.430.06731590.9960.0741
2.43-2.60.06329730.9950.0681
2.6-2.810.05827530.9960.0631
2.81-3.080.05525550.9950.061
3.08-3.440.05523210.9960.061
3.44-3.980.05420630.9960.061
3.98-4.870.05417600.9960.0581
4.87-6.890.05313740.9960.0581
6.89-19.70.0527720.9970.0581

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→19.7 Å / SU ML: 0.1266 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 2000 3.12 %
Rwork0.1618 62201 -
obs0.1623 64201 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 1.54→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 52 228 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01522498
X-RAY DIFFRACTIONf_angle_d1.35333411
X-RAY DIFFRACTIONf_chiral_restr0.0951395
X-RAY DIFFRACTIONf_plane_restr0.0128436
X-RAY DIFFRACTIONf_dihedral_angle_d20.077933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.21871420.20934387X-RAY DIFFRACTION99.76
1.58-1.620.24131410.19064397X-RAY DIFFRACTION99.93
1.62-1.670.18511410.18594396X-RAY DIFFRACTION100
1.67-1.720.19191420.1694422X-RAY DIFFRACTION99.93
1.72-1.780.20481420.16334417X-RAY DIFFRACTION99.96
1.78-1.860.16461420.15454406X-RAY DIFFRACTION99.98
1.86-1.940.17391410.15384404X-RAY DIFFRACTION99.71
1.94-2.040.18371430.16164415X-RAY DIFFRACTION99.65
2.04-2.170.20521410.16074414X-RAY DIFFRACTION99.5
2.17-2.340.18831430.16264436X-RAY DIFFRACTION99.7
2.34-2.570.19371420.17074431X-RAY DIFFRACTION99.98
2.57-2.940.17891450.17454504X-RAY DIFFRACTION99.89
2.94-3.70.17531450.15864509X-RAY DIFFRACTION99.85
3.7-19.70.16271500.14994663X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 0.271386725086 Å / Origin y: -28.5346881603 Å / Origin z: -20.1722573113 Å
111213212223313233
T0.138099131019 Å2-0.0184439502537 Å2-0.0138872559876 Å2-0.153180421892 Å20.0228403669651 Å2--0.150418728095 Å2
L1.06801024341 °2-0.298483401998 °20.0999283083193 °2-1.07773871144 °2-0.597858825207 °2--1.42810593675 °2
S-0.0532240513043 Å °0.0925904789948 Å °0.155433654691 Å °-0.00050070465508 Å °0.0319988432877 Å °0.00795158758214 Å °-0.0809749977515 Å °0.00163382411808 Å °0.00972634802233 Å °
Refinement TLS groupSelection details: all

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