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- PDB-8g5w: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -

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Basic information

Entry
Database: PDB / ID: 8g5w
TitleStructure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis complexed with native metal cofactor Mn++
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE-PRODUCT complex
Function / homology
Function and homology information


glycerol metabolic process / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / manganese ion binding / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded
Similarity search - Domain/homology
: / Fructose-1,6-bisphosphatase
Similarity search - Component
Biological speciesFrancisella cf. tularensis subsp. novicida 3523 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbad-Zapatero, C. / Selezneva, A.I.
Funding support2items
OrganizationGrant numberCountry
Other privatePotts Memorial Foundation G3541
Other privateChicago Biomedical Consortium 084679-00001
CitationJournal: Plos One / Year: 2023
Title: New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class.
Authors: Selezneva, A.I. / Harding, L.N.M. / Gutka, H.J. / Movahedzadeh, F. / Abad-Zapatero, C.
History
DepositionFeb 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase
B: Fructose-1,6-bisphosphatase
C: Fructose-1,6-bisphosphatase
D: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,99026
Polymers148,1124
Non-polymers1,87722
Water10,052558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complete tetramer in the a.u.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.845, 75.879, 77.616
Angle α, β, γ (deg.)67.831, 68.136, 76.372
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Fructose-1,6-bisphosphatase


Mass: 37028.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella cf. tularensis subsp. novicida 3523 (bacteria)
Gene: glpX, FNC33_05530, FNC42_07040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZJY0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Hampton Research PEG/Ion2 #14 8% Tacsimate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2022
RadiationMonochromator: Sillicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 83239 / % possible obs: 98 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Rsym value: 0.086 / Net I/σ(I): 24.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4064 / CC1/2: 0.808 / Rpim(I) all: 0.339 / Rrim(I) all: 0.653 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.37 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.4066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 4080 4.96 %
Rwork0.1607 78258 -
obs0.1628 82338 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.77 Å2
Refinement stepCycle: LAST / Resolution: 2→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9682 0 112 559 10353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01519874
X-RAY DIFFRACTIONf_angle_d1.424613285
X-RAY DIFFRACTIONf_chiral_restr0.06571553
X-RAY DIFFRACTIONf_plane_restr0.00861728
X-RAY DIFFRACTIONf_dihedral_angle_d18.19011424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.24321430.1952573X-RAY DIFFRACTION96.9
2.02-2.050.27161250.19352751X-RAY DIFFRACTION96.93
2.05-2.070.2411700.18642592X-RAY DIFFRACTION96.91
2.07-2.10.22611580.19042664X-RAY DIFFRACTION96.91
2.1-2.130.26351430.18392692X-RAY DIFFRACTION97.49
2.13-2.160.25281450.18452669X-RAY DIFFRACTION96.83
2.16-2.190.24471260.18432688X-RAY DIFFRACTION97.47
2.19-2.230.2431610.18092665X-RAY DIFFRACTION97.28
2.23-2.260.26661430.18342674X-RAY DIFFRACTION97.61
2.26-2.30.23941350.17832732X-RAY DIFFRACTION97.45
2.3-2.340.22861300.16812671X-RAY DIFFRACTION97.49
2.34-2.390.21311360.16182689X-RAY DIFFRACTION97.78
2.39-2.440.22691420.16192725X-RAY DIFFRACTION97.65
2.44-2.490.2231410.15562677X-RAY DIFFRACTION97.95
2.49-2.550.20851450.16232705X-RAY DIFFRACTION97.94
2.55-2.610.22381410.1622687X-RAY DIFFRACTION97.89
2.61-2.680.23271350.17082702X-RAY DIFFRACTION98.2
2.68-2.760.25851430.16622725X-RAY DIFFRACTION98.25
2.76-2.850.21831310.16722685X-RAY DIFFRACTION98.19
2.85-2.950.19591480.16462705X-RAY DIFFRACTION98.45
2.95-3.070.22831420.17562737X-RAY DIFFRACTION98.49
3.07-3.210.25031650.17252693X-RAY DIFFRACTION98.59
3.21-3.380.20091560.16112692X-RAY DIFFRACTION98.72
3.38-3.590.19681450.15322726X-RAY DIFFRACTION98.97
3.59-3.870.17241260.14732738X-RAY DIFFRACTION98.9
3.87-4.260.18391160.1372774X-RAY DIFFRACTION99.21
4.26-4.870.14921260.12722734X-RAY DIFFRACTION99.24
4.87-6.140.17461270.15952755X-RAY DIFFRACTION99.41
6.14-37.370.15511360.16652738X-RAY DIFFRACTION98.9

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