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Yorodumi- PDB-7txa: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7txa | |||||||||
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Title | Structure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis complexed with native metal cofactor Mn++ and product F6P | |||||||||
Components | Fructose-1,6-bisphosphataseFructose 1,6-bisphosphatase | |||||||||
Keywords | HYDROLASE/PRODUCT / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE / 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 / 6-O-phosphono-beta-D-fructofuranose / : / Fructose-1,6-bisphosphatase Function and homology information | |||||||||
Biological species | Francisella tularensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 7txa.cif.gz | 607.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7txa.ent.gz | 402.4 KB | Display | PDB format |
PDBx/mmJSON format | 7txa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txa ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txa | HTTPS FTP |
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-Related structure data
Related structure data | 7txbC 7txgC 8g5wC 8g5xC 7js3S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Sugar | #4: 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: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium malonate pH 6.0, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2021 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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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: 51.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.1 Å
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Refine LS restraints |
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LS refinement shell |
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