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Yorodumi- PDB-7js3: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7js3 | |||||||||
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Title | Structure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis | |||||||||
Components | Fructose-1,6-bisphosphataseFructose 1,6-bisphosphatase | |||||||||
Keywords | HYDROLASE / Class II FBPase / Gluconeogenesis / F. tularensis / antibacterial | |||||||||
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 / Fructose-1,6-bisphosphatase / 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. / Wolf, N.M. / Movahedzadeh, F. / Gutka, H. / Selezneva, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis. Authors: Selezneva, A.I. / Gutka, H.J. / Wolf, N.M. / Qurratulain, F. / 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 | 7js3.cif.gz | 260.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7js3.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 7js3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/7js3 ftp://data.pdbj.org/pub/pdb/validation_reports/js/7js3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ayuS S: Starting model for refinement |
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Similar structure data |
-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 tularensis (bacteria) / Gene: glpX, EGT35_01410, FNC33_05530, FNC42_07040 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2ZJY0, UniProt: Q5NEJ8*PLUS #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #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: 2.4 Å3/Da / Density % sol: 51.23 % / Description: Prismatic needles |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 20 mM Tricine pH 7.8, 50 mM KCl, 1 mM MgCl2, 0.1 mM DTT, 15% glycerol; Composition of reservoir solution 0.2 M sodium formate, 20% PEG 3350; Volume and ratio of drop 22.4 uL (1:1) Volume of reservoir (ul) 100 |
-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: 0.92456 Å | ||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2017 | ||||||||||||||||||
Radiation | Monochromator: Si (1111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.92456 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→40 Å / Num. obs: 53682 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 42.9 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.106 / Rsym value: 0.106 / Net I/σ(I): 24.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2620 / CC1/2: 0.673 / Rpim(I) all: 0.276 / Rrim(I) all: 0.531 / Rsym value: 0.531 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ayu Resolution: 2.4→38.11 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.495 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1 / ESU R: 0.074 / ESU R Free: 0.044 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.033 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→38.11 Å
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Refine LS restraints |
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LS refinement shell |
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