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Yorodumi- PDB-3big: Crystal structure of the fructose-1,6-bisphosphatase GlpX from E.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3big | ||||||
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Title | Crystal structure of the fructose-1,6-bisphosphatase GlpX from E.coli in complex with inorganic phosphate | ||||||
Components | Fructose-1,6-bisphosphatase class II glpX | ||||||
Keywords | HYDROLASE / GlpX / 1 / 6-bisphosphatase / carbohydrate metabolism / Manganese | ||||||
Function / homology | Function and homology information glycerol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / manganese ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Lunin, V.V. / Skarina, T. / Brown, G. / Yakunin, A.F. / Edwards, A.M. / Savchenko, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli. Authors: Brown, G. / Singer, A. / Lunin, V.V. / Proudfoot, M. / Skarina, T. / Flick, R. / Kochinyan, S. / Sanishvili, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3big.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3big.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3big.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3big ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3big | HTTPS FTP |
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-Related structure data
Related structure data | 1ni9SC 3bihC 3d1rC 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
#1: Protein | Mass: 36046.492 Da / Num. of mol.: 1 / Mutation: D61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpX, b3925, JW3896 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A9C9, fructose-bisphosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 400, 0.2M CaCl2, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. all: 33731 / Num. obs: 33731 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.056 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 3105 / Rsym value: 0.55 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NI9 Resolution: 1.85→40.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.805 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.743 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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