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

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Basic information

Entry
Database: PDB / ID: 7txa
TitleStructure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis complexed with native metal cofactor Mn++ and product F6P
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE/PRODUCT / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE / 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 / metal 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
6-O-phosphono-beta-D-fructofuranose / : / Fructose-1,6-bisphosphatase
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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 / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Q: Fructose-1,6-bisphosphatase
U: Fructose-1,6-bisphosphatase
W: Fructose-1,6-bisphosphatase
1: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,34921
Polymers296,2248
Non-polymers1,12513
Water7,152397
1
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)148,70211
Polymers148,1124
Non-polymers5907
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-32 kcal/mol
Surface area45070 Å2
MethodPISA
2
Q: Fructose-1,6-bisphosphatase
U: Fructose-1,6-bisphosphatase
W: Fructose-1,6-bisphosphatase
1: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,64710
Polymers148,1124
Non-polymers5356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-23 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.394, 76.628, 141.465
Angle α, β, γ (deg.)76.839, 87.235, 75.707
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.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: glpX, EGT35_01410, FNC33_05530, FNC42_07040 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2ZJY0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium malonate pH 6.0, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2021
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→39.1 Å / Num. obs: 101338 / % possible obs: 98.38 % / Redundancy: 3 % / Biso Wilson estimate: 42.17 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.042 / Rrim(I) all: 0.075 / Rsym value: 0.043 / Net I/σ(I): 17.55
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / Num. unique obs: 9973 / CC1/2: 0.75 / Rpim(I) all: 0.32 / Rrim(I) all: 0.55 / Rsym value: 0.39 / Χ2: 0.75 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5refinement
MOLREPphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7js3

7js3


Resolution: 2.4→39.1 Å / SU ML: 0.3292 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.3821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 5064 5 %
Rwork0.1958 96217 -
obs0.1984 101281 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19347 0 43 397 19787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009119587
X-RAY DIFFRACTIONf_angle_d1.197626435
X-RAY DIFFRACTIONf_chiral_restr0.06473115
X-RAY DIFFRACTIONf_plane_restr0.00653459
X-RAY DIFFRACTIONf_dihedral_angle_d16.60272777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.35891760.27463120X-RAY DIFFRACTION97.63
2.43-2.460.29691820.27223245X-RAY DIFFRACTION97.72
2.46-2.490.3391800.26573145X-RAY DIFFRACTION97.85
2.49-2.520.3291750.26783190X-RAY DIFFRACTION98.02
2.52-2.550.31121610.25963224X-RAY DIFFRACTION98.06
2.55-2.590.31261600.23923144X-RAY DIFFRACTION97.84
2.59-2.620.31251550.24553228X-RAY DIFFRACTION98.14
2.62-2.660.28261590.24533231X-RAY DIFFRACTION98.12
2.66-2.70.33121690.25263173X-RAY DIFFRACTION98.21
2.7-2.750.34361590.25313238X-RAY DIFFRACTION98.18
2.75-2.790.29791640.2473154X-RAY DIFFRACTION98.4
2.79-2.850.2751560.24133266X-RAY DIFFRACTION98.5
2.85-2.90.3041400.24353217X-RAY DIFFRACTION98.36
2.9-2.960.33021750.25173211X-RAY DIFFRACTION98.37
2.96-3.020.30431600.23873205X-RAY DIFFRACTION98.48
3.02-3.090.34691800.24633179X-RAY DIFFRACTION98.71
3.09-3.170.29751730.23433223X-RAY DIFFRACTION98.55
3.17-3.260.26122060.22573169X-RAY DIFFRACTION98.66
3.26-3.350.30211850.2153199X-RAY DIFFRACTION98.66
3.35-3.460.25371710.20533205X-RAY DIFFRACTION98.74
3.46-3.580.23431810.20133194X-RAY DIFFRACTION98.83
3.58-3.730.24971630.18683245X-RAY DIFFRACTION98.93
3.73-3.90.23331400.1713273X-RAY DIFFRACTION98.87
3.9-4.10.21531750.1783192X-RAY DIFFRACTION99.06
4.1-4.360.21611820.15633233X-RAY DIFFRACTION99.22
4.36-4.70.15491580.14213257X-RAY DIFFRACTION99.16
4.7-5.170.22411610.15693236X-RAY DIFFRACTION99.1
5.17-5.910.251560.17143263X-RAY DIFFRACTION99.22
5.91-7.440.18541870.15923193X-RAY DIFFRACTION99.27
7.44-39.10.17421750.14873165X-RAY DIFFRACTION97.43

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