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Yorodumi- PDB-8g5x: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g5x | |||||||||
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Title | Structure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis complexed with native metal cofactor Mn++ and substrate Fructose-1,6-Bisphosphate | |||||||||
Components | Fructose-1,6-bisphosphataseFructose 1,6-bisphosphatase | |||||||||
Keywords | HYDROLASE / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE-PRODUCT complex | |||||||||
Function / homology | Fructose-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 / 1,6-di-O-phosphono-beta-D-fructofuranose / : / Fructose-1,6-bisphosphatase Function and homology information | |||||||||
Biological species | Francisella cf. tularensis subsp. novicida 3523 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Abad-Zapatero, C. / Selezneva, A.I. | |||||||||
Funding support | 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g5x.cif.gz | 586.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g5x.ent.gz | 393.8 KB | Display | PDB format |
PDBx/mmJSON format | 8g5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/8g5x ftp://data.pdbj.org/pub/pdb/validation_reports/g5/8g5x | HTTPS FTP |
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-Related structure data
Related structure data | 7txaC 7txbC 7txgC 8g5wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-MN / #4: Sugar | ChemComp-FBP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Hampton Research PEG/Ion2 #30, 0.2 M Ammonium Tartrate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 59766 / % possible obs: 97.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.054 / Rrim(I) all: 0.527 / Rsym value: 0.059 / Net I/σ(I): 20.92 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 2923 / CC1/2: 0.757 / Rpim(I) all: 0.356 / Rrim(I) all: 0.527 / Rsym value: 0.386 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.18 Å / SU ML: 0.2371 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.2482 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.18 Å
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Refine LS restraints |
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LS refinement shell |
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