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

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Basic information

Entry
Database: PDB / ID: 7fca
TitlePfkB(Mycobacterium marinum)
Components(Fructokinase, PfkB) x 2
KeywordsOXIDOREDUCTASE / PfkB / kinase / sandwich
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
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.
History
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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)189,70616
Polymers188,7706
Non-polymers93510
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
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

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Components

#1: Protein
Fructokinase, PfkB /


Mass: 31707.805 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: pfkB, MMAR_4574 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEF4
#2: Protein Fructokinase, PfkB /


Mass: 30231.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: pfkB, MMAR_4574 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEF4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: pH 6.9, 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.21→66.92 Å / Num. obs: 104442 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 55.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.84
Reflection shellResolution: 2.21→2.286 Å / Num. unique obs: 10403 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U7X

4u7x


Resolution: 2.21→66.92 Å / SU ML: 0.2895 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2678 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2452 5123 4.91 %
Rwork0.212 99319 -
obs0.2136 104442 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.07 Å2
Refinement stepCycle: LAST / Resolution: 2.21→66.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11739 0 55 161 11955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009111979
X-RAY DIFFRACTIONf_angle_d1.032616413
X-RAY DIFFRACTIONf_chiral_restr0.06192017
X-RAY DIFFRACTIONf_plane_restr0.00692144
X-RAY DIFFRACTIONf_dihedral_angle_d26.934135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.230.30621720.27993264X-RAY DIFFRACTION99.71
2.23-2.260.33981570.27523315X-RAY DIFFRACTION99.91
2.26-2.290.3541580.27283320X-RAY DIFFRACTION99.94
2.29-2.310.32881730.2593296X-RAY DIFFRACTION100
2.31-2.340.28841830.2623275X-RAY DIFFRACTION99.91
2.34-2.380.31281640.25283344X-RAY DIFFRACTION99.89
2.38-2.410.29521840.2533281X-RAY DIFFRACTION99.97
2.41-2.450.30091740.24843296X-RAY DIFFRACTION100
2.45-2.490.28111690.25463325X-RAY DIFFRACTION99.94
2.49-2.530.28561650.25863278X-RAY DIFFRACTION100
2.53-2.570.31582030.24863308X-RAY DIFFRACTION100
2.57-2.620.3131730.25353272X-RAY DIFFRACTION99.97
2.62-2.670.30411710.2593325X-RAY DIFFRACTION99.94
2.67-2.720.2791830.25373323X-RAY DIFFRACTION99.94
2.72-2.780.26431640.25073292X-RAY DIFFRACTION99.97
2.78-2.840.29211660.24833335X-RAY DIFFRACTION100
2.84-2.920.32871770.26253293X-RAY DIFFRACTION99.97
2.92-2.990.31271870.25653315X-RAY DIFFRACTION99.94
2.99-3.080.33871630.26063301X-RAY DIFFRACTION99.91
3.08-3.180.26391470.25153310X-RAY DIFFRACTION99.88
3.18-3.30.25891800.23113340X-RAY DIFFRACTION99.97
3.3-3.430.29531880.23543300X-RAY DIFFRACTION100
3.43-3.580.26331720.2153323X-RAY DIFFRACTION99.91
3.58-3.770.25182040.2133269X-RAY DIFFRACTION99.91
3.77-4.010.2371770.19873298X-RAY DIFFRACTION99.91
4.01-4.320.19211430.17853396X-RAY DIFFRACTION100
4.32-4.750.1741740.1583311X-RAY DIFFRACTION99.69
4.75-5.440.21781450.18213346X-RAY DIFFRACTION99.91
5.44-6.850.20731530.19753387X-RAY DIFFRACTION99.89
6.85-66.920.19571540.17853281X-RAY DIFFRACTION95.84

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