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- PDB-9cit: Crystal structure of pyrophosphate-dependent phosphofructokinase ... -

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Basic information

Entry
Database: PDB / ID: 9cit
TitleCrystal structure of pyrophosphate-dependent phosphofructokinase from Candidatus Prometheoarchaeum syntrophicum with phosphoenolpyruvate, phosphate and Mg2+
Components6-phosphofructokinase
KeywordsTRANSFERASE / 2.7.1.90 / phosphofructokinase / phosphotransferase / Rossman fold
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase
Similarity search - Domain/homology
PHOSPHOENOLPYRUVATE / PHOSPHATE ION / 6-phosphofructokinase
Similarity search - Component
Biological speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsCompton, J.A. / Yosaatmadja, Y. / Bashiri, G. / Vickers, C.J. / Patrick, W.M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: To Be Published
Title: Structure and function of an unusual, multi-tasking phosphofructokinase from an Asgard archaeon
Authors: Compton, J.A. / Yosaatmadja, Y. / Bashiri, G. / Vickers, C.J. / Patrick, W.M.
History
DepositionJul 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 6-phosphofructokinase
A: 6-phosphofructokinase
C: 6-phosphofructokinase
D: 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,90613
Polymers187,1174
Non-polymers7899
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-129 kcal/mol
Surface area50190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.577, 71.995, 136.754
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
6-phosphofructokinase


Mass: 46779.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea)
Gene: DSAG12_00460 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9D762
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1 M MMT pH 9.0, 30 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.57→45.58 Å / Num. obs: 53047 / % possible obs: 99.27 % / Redundancy: 14 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 19.1
Reflection shellResolution: 2.57→2.66 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4220 / Rpim(I) all: 0.2 / Rrim(I) all: 0.76 / % possible all: 93.64

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→45.58 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 32.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 2629 4.96 %
Rwork0.2159 --
obs0.2189 52988 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10959 0 43 27 11029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711189
X-RAY DIFFRACTIONf_angle_d0.92515265
X-RAY DIFFRACTIONf_dihedral_angle_d6.5581624
X-RAY DIFFRACTIONf_chiral_restr0.0521816
X-RAY DIFFRACTIONf_plane_restr0.0071979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.620.4036980.29692314X-RAY DIFFRACTION86
2.62-2.670.38371380.27292681X-RAY DIFFRACTION100
2.67-2.720.35761240.25752606X-RAY DIFFRACTION100
2.72-2.780.37531430.23882647X-RAY DIFFRACTION100
2.78-2.840.31841360.23912658X-RAY DIFFRACTION100
2.84-2.920.3411570.25612637X-RAY DIFFRACTION100
2.92-2.990.35591540.2612632X-RAY DIFFRACTION100
2.99-3.080.31721300.25232647X-RAY DIFFRACTION100
3.08-3.180.29271350.24782682X-RAY DIFFRACTION100
3.18-3.30.31851430.25182659X-RAY DIFFRACTION100
3.3-3.430.33181250.25122708X-RAY DIFFRACTION100
3.43-3.580.33691470.25162628X-RAY DIFFRACTION100
3.58-3.770.28061180.22612673X-RAY DIFFRACTION100
3.77-4.010.26261420.2082693X-RAY DIFFRACTION100
4.01-4.320.22971510.18342658X-RAY DIFFRACTION100
4.32-4.750.24871540.17192672X-RAY DIFFRACTION100
4.75-5.440.24081410.1792671X-RAY DIFFRACTION100
5.44-6.850.26131400.22552716X-RAY DIFFRACTION100
6.85-45.580.19111530.18162777X-RAY DIFFRACTION100

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