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

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Basic information

Entry
Database: PDB / ID: 9cir
TitleCrystal structure of pyrophosphate-dependent phosphofructokinase from Candidatus Prometheoarchaeum syntrophicum
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 / monosaccharide binding / fructose 6-phosphate metabolic process / 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-phosphofructokinase
Similarity search - Component
Biological speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
A: 6-phosphofructokinase
B: 6-phosphofructokinase
C: 6-phosphofructokinase
D: 6-phosphofructokinase


Theoretical massNumber of molelcules
Total (without water)187,1174
Polymers187,1174
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-82 kcal/mol
Surface area50590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.180, 71.404, 134.868
Angle α, β, γ (deg.)90.00, 91.12, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.87 %
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: 2.2→49.02 Å / Num. obs: 82545 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.13 / Rrim(I) all: 0.47 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 4539 / Rpim(I) all: 3.55 / Rrim(I) all: 13.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.02 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 4155 5.04 %
Rwork0.2362 --
obs0.2389 82466 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11005 0 0 221 11226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811204
X-RAY DIFFRACTIONf_angle_d0.95615250
X-RAY DIFFRACTIONf_dihedral_angle_d6.1031610
X-RAY DIFFRACTIONf_chiral_restr0.0561804
X-RAY DIFFRACTIONf_plane_restr0.0061969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.35361540.30362607X-RAY DIFFRACTION100
2.23-2.250.37751200.30652586X-RAY DIFFRACTION100
2.25-2.280.31741560.29362549X-RAY DIFFRACTION100
2.28-2.310.37481160.2852670X-RAY DIFFRACTION100
2.31-2.340.37861370.29232554X-RAY DIFFRACTION100
2.34-2.370.35911480.28772621X-RAY DIFFRACTION100
2.37-2.40.31131590.27612523X-RAY DIFFRACTION100
2.4-2.440.32071330.26482616X-RAY DIFFRACTION100
2.44-2.480.31971530.25222577X-RAY DIFFRACTION100
2.48-2.520.34961140.2622609X-RAY DIFFRACTION100
2.52-2.560.3291380.26662598X-RAY DIFFRACTION100
2.56-2.610.33281340.26042584X-RAY DIFFRACTION100
2.61-2.660.34271420.26012632X-RAY DIFFRACTION100
2.66-2.710.31831600.25962583X-RAY DIFFRACTION100
2.71-2.770.27541470.24462592X-RAY DIFFRACTION100
2.77-2.840.32471420.2422597X-RAY DIFFRACTION100
2.84-2.910.36461130.25392598X-RAY DIFFRACTION100
2.91-2.990.35731300.2572654X-RAY DIFFRACTION100
2.99-3.070.33021510.2552585X-RAY DIFFRACTION100
3.07-3.170.28531420.24492583X-RAY DIFFRACTION100
3.17-3.290.33361260.24912644X-RAY DIFFRACTION100
3.29-3.420.29541250.25072603X-RAY DIFFRACTION100
3.42-3.570.2731320.23022652X-RAY DIFFRACTION100
3.57-3.760.28191260.22422618X-RAY DIFFRACTION100
3.76-40.27051300.22342624X-RAY DIFFRACTION100
4-4.310.27491660.20752589X-RAY DIFFRACTION100
4.31-4.740.2311410.19742652X-RAY DIFFRACTION100
4.74-5.420.26541390.21422634X-RAY DIFFRACTION100
5.42-6.830.24711310.24942660X-RAY DIFFRACTION100
6.83-49.020.25251500.21022717X-RAY DIFFRACTION99

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