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- PDB-9cis: Crystal structure of the pyrophosphate-dependent phosphofructokin... -

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Basic information

Entry
Database: PDB / ID: 9cis
TitleCrystal structure of the pyrophosphate-dependent phosphofructokinase from Candidatus Prometheoarchaeum syntrophicum with fructose 6-phosphate
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
6-O-phosphono-beta-D-fructofuranose / 6-phosphofructokinase
Similarity search - Component
Biological speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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)188,1588
Polymers187,1174
Non-polymers1,0414
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14640 Å2
ΔGint-94 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.210, 71.866, 136.530
Angle α, β, γ (deg.)90.00, 91.08, 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: 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.: 4 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1 M MMT pH 9.0, 25 % 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: 2.35→45.5 Å / Num. obs: 69107 / % possible obs: 99.78 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.08 / Rrim(I) all: 0.3 / Net I/σ(I): 8
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 8.63 / Num. unique obs: 4391 / Rpim(I) all: 2.35 / Rrim(I) all: 8.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.5 Å / SU ML: 0.45 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3144 3397 4.93 %
Rwork0.2437 --
obs0.2471 68953 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10539 0 64 85 10688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810792
X-RAY DIFFRACTIONf_angle_d0.97914748
X-RAY DIFFRACTIONf_dihedral_angle_d6.4941587
X-RAY DIFFRACTIONf_chiral_restr0.0531763
X-RAY DIFFRACTIONf_plane_restr0.0081911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.4311340.38162701X-RAY DIFFRACTION99
2.38-2.420.36431550.34642678X-RAY DIFFRACTION100
2.42-2.460.37861340.32252713X-RAY DIFFRACTION100
2.46-2.50.40611700.32112717X-RAY DIFFRACTION100
2.5-2.540.39841570.31512658X-RAY DIFFRACTION100
2.54-2.590.39571360.31252725X-RAY DIFFRACTION100
2.59-2.640.36751230.30072714X-RAY DIFFRACTION100
2.64-2.690.33911350.29882751X-RAY DIFFRACTION100
2.69-2.750.35391380.29182731X-RAY DIFFRACTION100
2.75-2.810.33311430.27592680X-RAY DIFFRACTION100
2.81-2.880.35011750.27632724X-RAY DIFFRACTION100
2.88-2.960.35551350.26312722X-RAY DIFFRACTION100
2.96-3.050.32381690.2612702X-RAY DIFFRACTION100
3.05-3.150.36161450.26182721X-RAY DIFFRACTION100
3.15-3.260.30361440.25422749X-RAY DIFFRACTION100
3.26-3.390.31381460.25082703X-RAY DIFFRACTION100
3.39-3.540.31091230.24632739X-RAY DIFFRACTION100
3.54-3.730.30561270.22532754X-RAY DIFFRACTION100
3.73-3.960.30571560.22322739X-RAY DIFFRACTION100
3.96-4.270.29121280.21022749X-RAY DIFFRACTION100
4.27-4.70.25371320.20562760X-RAY DIFFRACTION100
4.7-5.380.29781300.22332776X-RAY DIFFRACTION100
5.38-6.770.33561290.26522774X-RAY DIFFRACTION100
6.77-45.50.27851330.2122876X-RAY DIFFRACTION100

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