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Yorodumi- PDB-5eyn: Crystal structure of Fructokinase from Vibrio cholerae O395 in fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eyn | ||||||
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Title | Crystal structure of Fructokinase from Vibrio cholerae O395 in fructose, ADP, Beryllium trifluoride and calcium ion bound form | ||||||
Components | Fructokinase | ||||||
Keywords | TRANSFERASE / kinase / fructose | ||||||
Function / homology | Function and homology information fructokinase / ketohexokinase activity / fructokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin ...fructokinase / ketohexokinase activity / fructokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.289 Å | ||||||
Authors | Paul, R. / Nath, S. / Sen, U. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Fructokinase from Vibrio cholerae O395 in apo form Authors: Paul, R. / Nath, S. / Sen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eyn.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eyn.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 5eyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eyn_validation.pdf.gz | 838.7 KB | Display | wwPDB validaton report |
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Full document | 5eyn_full_validation.pdf.gz | 840.2 KB | Display | |
Data in XML | 5eyn_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5eyn_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/5eyn ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5eyn | HTTPS FTP |
-Related structure data
Related structure data | 5ey7C 5f0zC 5f11C 1tz6S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 34995.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: cscK, VC0395_0600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AER7, fructokinase |
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#2: Sugar | ChemComp-FRU / |
-Non-polymers , 5 types, 383 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-BEF / |
#5: Chemical | ChemComp-ADP / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 5% PEG 6000, 0.1M MES, pH 6.0 as precipitant and VcFK (complex with 5 mM ADP + 5 mM Fructose ) + 5 mM BeF3 (soaked) PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.289→32.15 Å / Num. obs: 71986 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.29→1.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.35 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tz6 Resolution: 1.289→32.15 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.289→32.15 Å
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Refine LS restraints |
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LS refinement shell |
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