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- PDB-7txg: Structure of the Class II Fructose-1,6-Bisphosphatase from Franci... -

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Basic information

Entry
Database: PDB / ID: 7txg
TitleStructure of the Class II Fructose-1,6-Bisphosphatase from Francisella tularensis with native Mn++ divalent cation and partially occupied product F6P
ComponentsFructose-1,6-bisphosphataseFructose 1,6-bisphosphatase
KeywordsHYDROLASE / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets
Function / homologyFructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded / glycerol metabolic process / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding / : / PHOSPHATE ION / Fructose-1,6-bisphosphatase
Function and homology information
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAbad-Zapatero, C. / Selezneva, A.I. / Harding, L.N.M. / Movahedzadeh, F.
Funding support1items
OrganizationGrant numberCountry
Other privatePotts Memorial Foundation G3541
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 9, 2022Deposition 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: 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)149,63022
Polymers148,1124
Non-polymers1,51818
Water12,394688
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, A similar assembly has been found in the previously released structure 7js3
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.176, 76.226, 77.924
Angle α, β, γ (deg.)68.024, 68.223, 76.649
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 / Fructose 1,6-bisphosphatase


Mass: 37028.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: glpX, FNC33_05530, FNC42_07040 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2ZJY0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% Tacsimate pH 6.0 and 20% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 85208 / % possible obs: 85.87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.054 / Rrim(I) all: 0.077 / Rsym value: 0.054 / Net I/σ(I): 25.27
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.6 / Num. unique obs: 8144 / CC1/2: 0.94 / Rpim(I) all: 0.15 / Rrim(I) all: 0.208 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7js3

7js3


Resolution: 1.9→19.94 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.2677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 4208 4.94 %
Rwork0.187 80983 -
obs0.1887 85191 85.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9720 0 91 689 10500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00769894
X-RAY DIFFRACTIONf_angle_d0.915213324
X-RAY DIFFRACTIONf_chiral_restr0.06041558
X-RAY DIFFRACTIONf_plane_restr0.00481736
X-RAY DIFFRACTIONf_dihedral_angle_d21.87783642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.26711040.22812163X-RAY DIFFRACTION69.93
1.92-1.950.29951410.22232772X-RAY DIFFRACTION87.27
1.95-1.970.26151570.21662804X-RAY DIFFRACTION90.08
1.97-20.28911550.20722825X-RAY DIFFRACTION89.81
2-2.020.2331430.20392860X-RAY DIFFRACTION91.55
2.02-2.050.24491330.20742902X-RAY DIFFRACTION90.71
2.05-2.080.24481480.20182842X-RAY DIFFRACTION90.52
2.08-2.110.24551280.1992852X-RAY DIFFRACTION90.77
2.11-2.140.2451630.19332842X-RAY DIFFRACTION90.9
2.14-2.180.23031400.19562864X-RAY DIFFRACTION90.21
2.18-2.220.27471650.20132778X-RAY DIFFRACTION89.94
2.22-2.260.24381480.20832798X-RAY DIFFRACTION89.65
2.26-2.30.23381440.20312868X-RAY DIFFRACTION89.01
2.3-2.350.23611520.19352697X-RAY DIFFRACTION87.99
2.35-2.40.24871260.18852769X-RAY DIFFRACTION87.3
2.4-2.450.23931480.19212760X-RAY DIFFRACTION86.99
2.45-2.510.25251350.19172681X-RAY DIFFRACTION85.28
2.51-2.580.25421450.20342523X-RAY DIFFRACTION81.32
2.58-2.660.23251150.1932273X-RAY DIFFRACTION72.54
2.66-2.740.26451360.20412607X-RAY DIFFRACTION82.87
2.74-2.840.24761470.20482847X-RAY DIFFRACTION90.64
2.84-2.950.24921520.2022842X-RAY DIFFRACTION90.64
2.95-3.090.29811580.20412849X-RAY DIFFRACTION90.14
3.09-3.250.20371440.20192777X-RAY DIFFRACTION88.43
3.25-3.450.21221390.18472708X-RAY DIFFRACTION86.43
3.45-3.720.20191400.17582685X-RAY DIFFRACTION85.71
3.72-4.090.19881270.16592558X-RAY DIFFRACTION81.04
4.09-4.670.15931310.15592254X-RAY DIFFRACTION72.62
4.67-5.860.18151130.16922334X-RAY DIFFRACTION73.37
5.86-19.940.16951310.16232649X-RAY DIFFRACTION84.37

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