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- PDB-7txb: Structure of the Class II Fructose-1,6-Bisphophatase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 7txb
TitleStructure of the Class II Fructose-1,6-Bisphophatase from Mycobacterium tuberculosis complexed with substrate F1,6BP
ComponentsFructose-1,6-bisphosphatase class 2
KeywordsHYDROLASE/SUBSTRATE / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


glycerol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / Fructose-1,6-bisphosphatase class 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsAbad-Zapatero, C. / Selezneva, A.I. / Gutka, H.J.
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 8, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Fructose-1,6-bisphosphatase class 2
A: Fructose-1,6-bisphosphatase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2348
Polymers73,3212
Non-polymers9136
Water81145
1
B: Fructose-1,6-bisphosphatase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1174
Polymers36,6601
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fructose-1,6-bisphosphatase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1174
Polymers36,6601
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.110, 117.110, 325.917
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Fructose-1,6-bisphosphatase class 2 / FBPase class 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase class 2


Mass: 36660.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glpX, MRA_1110 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5U1E6, fructose-bisphosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.4 Å3/Da / Density % sol: 72.04 % / Description: hexagonal bipyramids
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 2.9 M Sodium Malonate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.71→20 Å / Num. obs: 14655 / % possible obs: 98.64 % / Redundancy: 18.4 % / Biso Wilson estimate: 88.91 Å2 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.14 / Rsym value: 0.2 / Net I/σ(I): 11
Reflection shellResolution: 3.71→3.84 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 656 / Rrim(I) all: 0.427 / Rsym value: 0.678 / % possible all: 89.76

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ayu

6ayu


Resolution: 3.71→19.99 Å / SU ML: 0.3546 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2734 736 5.07 %
Rwork0.2126 13784 -
obs0.2155 14520 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.19 Å2
Refinement stepCycle: LAST / Resolution: 3.71→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 54 45 4587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034598
X-RAY DIFFRACTIONf_angle_d0.61656228
X-RAY DIFFRACTIONf_chiral_restr0.045719
X-RAY DIFFRACTIONf_plane_restr0.0042819
X-RAY DIFFRACTIONf_dihedral_angle_d23.8165673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.71-3.990.36991310.29022537X-RAY DIFFRACTION93.38
3.99-4.390.3141560.22922709X-RAY DIFFRACTION99.83
4.39-5.010.22071740.18742735X-RAY DIFFRACTION100
5.01-6.280.28831420.23352805X-RAY DIFFRACTION100
6.29-19.990.24551330.1822998X-RAY DIFFRACTION99.81

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