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- PDB-7cf8: PfkB(Mycobacterium marinum) -

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Basic information

Database: PDB / ID: 7cf8
TitlePfkB(Mycobacterium marinum)
ComponentsFructokinase, PfkB
KeywordsOXIDOREDUCTASE / PfkB / kinase / momer / sandwich / HYDROLASE
Function / homology
Function and homology information

phosphotransferase activity, alcohol group as acceptor / kinase activity / phosphorylation
Similarity search - Function
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
PHOSPHATE ION / Fructokinase, PfkB
Similarity search - Component
Biological speciesMycobacterium marinum (unknown)
AuthorsLi, J. / Gao, B. / Ji, R.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum.
Authors: Gao, B. / Ji, R. / Li, Z. / Su, X. / Li, H. / Sun, Y. / Ji, C. / Gan, J. / Li, J.
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Fructokinase, PfkB
B: Fructokinase, PfkB
C: Fructokinase, PfkB
D: Fructokinase, PfkB
E: Fructokinase, PfkB
F: Fructokinase, PfkB
hetero molecules

Theoretical massNumber of molelcules
Total (without water)190,81814

  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.415, 125.406, 137.518
Angle α, β, γ (deg.)90.000, 106.834, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z


#1: Protein
Fructokinase, PfkB /

Mass: 31677.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (unknown)
Strain: ATCC BAA-535 / M / Gene: pfkB, MMAR_4574 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEF4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate

Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole, 1.0M (NH4)2HPO4, pH 8.0

Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2066→131.625 Å / Num. obs: 104443 / % possible obs: 99.79 % / Redundancy: 2 % / Biso Wilson estimate: 55.02 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.84
Reflection shellResolution: 2.207→2.286 Å / Num. unique obs: 10404 / CC1/2: 0.999


HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u7x
Resolution: 2.21→66.92 Å / SU ML: 0.3076 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3221 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2474 5124 4.91 %
Rwork0.2183 99319 -
obs0.2197 104443 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.8 Å2
Refinement stepCycle: LAST / Resolution: 2.21→66.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11674 0 43 156 11873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015611899
X-RAY DIFFRACTIONf_angle_d1.890116311
X-RAY DIFFRACTIONf_chiral_restr0.15212014
X-RAY DIFFRACTIONf_plane_restr0.00882130
X-RAY DIFFRACTIONf_dihedral_angle_d26.79034073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.230.32241720.29563264X-RAY DIFFRACTION99.71
2.23-2.260.32821570.2913315X-RAY DIFFRACTION99.91
2.26-2.290.37591580.28293320X-RAY DIFFRACTION99.94
2.29-2.310.34991730.27853296X-RAY DIFFRACTION100
2.31-2.340.29131830.27573275X-RAY DIFFRACTION99.91
2.34-2.380.34391640.26813344X-RAY DIFFRACTION99.89
2.38-2.410.33721840.26953281X-RAY DIFFRACTION99.97
2.41-2.450.29151740.26043296X-RAY DIFFRACTION100
2.45-2.490.31021690.26453325X-RAY DIFFRACTION99.94
2.49-2.530.30011650.27663278X-RAY DIFFRACTION100
2.53-2.570.32772030.2553308X-RAY DIFFRACTION100
2.57-2.620.32351730.2613272X-RAY DIFFRACTION99.97
2.62-2.670.3181710.25833325X-RAY DIFFRACTION99.94
2.67-2.720.28821830.25833323X-RAY DIFFRACTION99.94
2.72-2.780.2671640.24923292X-RAY DIFFRACTION99.97
2.78-2.840.31291660.24413335X-RAY DIFFRACTION100
2.84-2.920.34171770.2653293X-RAY DIFFRACTION99.97
2.92-2.990.32651870.26043315X-RAY DIFFRACTION99.94
2.99-3.080.33951630.27113301X-RAY DIFFRACTION99.91
3.08-3.180.29661470.24773310X-RAY DIFFRACTION99.88
3.18-3.30.27791800.23563340X-RAY DIFFRACTION99.97
3.3-3.430.29191880.23833300X-RAY DIFFRACTION100
3.43-3.580.25731720.21693323X-RAY DIFFRACTION99.91
3.58-3.770.26052040.21753269X-RAY DIFFRACTION99.91
3.77-4.010.22341770.20493298X-RAY DIFFRACTION99.91
4.01-4.320.19791430.18393396X-RAY DIFFRACTION100
4.32-4.750.16591740.16593311X-RAY DIFFRACTION99.69
4.75-5.440.20731450.18733346X-RAY DIFFRACTION99.91
5.44-6.850.19751530.19753387X-RAY DIFFRACTION99.89
6.85-66.920.19321550.18953281X-RAY DIFFRACTION95.87

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