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Yorodumi- PDB-1e46: L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant E73S -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+46 | ||||||
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Title | L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant E73S | ||||||
Components | L-FUCULOSE 1-PHOSPHATE ALDOLASE | ||||||
Keywords | ALDOLASE (CLASS II) / BACTERIAL L-FUCOSE METABOLISM / CLEAVAGE OF L-FUCULOSE 1-PHOSPHATE TO DIHYDROXYACETONE PHOSPHATE AND L-LACTALDEHYDE / MUTANT STRUCTURE | ||||||
Function / homology | Function and homology information D-arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / L-fucose catabolic process / pentose catabolic process / aldehyde-lyase activity / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.55 Å | ||||||
Authors | Joerger, A.C. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis Authors: Joerger, A.C. / Mueller-Dieckmann, C. / Schulz, G.E. #1: Journal: Biochemistry / Year: 2000 Title: Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived by Structure-Directed Mutagenesis Authors: Joerger, A.C. / Gosse, C. / Fessner, W.-D. / Schulz, G.E. #2: Journal: J.Mol.Biol. / Year: 1996 Title: Catalytic Mechanism of the Metal-Dependent Fuculose Aldolase from Escherichia Coli as Derived from the Structure Authors: Dreyer, M.K. / Schulz, G.E. #3: Journal: J.Mol.Biol. / Year: 1993 Title: The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli Authors: Dreyer, M.K. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e46.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e46.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 1e46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e46 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e46 | HTTPS FTP |
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-Related structure data
Related structure data | 1e47C 1e48C 1e49C 1e4aC 1e4bC 1e4cC C: citing same article (ref.) |
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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
#1: Protein | Mass: 23763.283 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) Description: E73S MUTATION PERFORMED WITH PHOSPHOROTHIOATE METHOD USING M13MP19 Plasmid: PKKFA2-E73S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105 References: UniProt: P11550, UniProt: P0AB87*PLUS, L-fuculose-phosphate aldolase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Compound details | CHAIN P ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALS GROWN FROM AMMONIUM SULFATE AT PH 8.0, VAPOUR DIFFUSION, HANGING DROP, CONDITIONS CLOSE TO THE ONES REPORTED FOR THE WILD-TYPE, SEE PDB ID 1FUA FOR FURTHER DETAILS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.6 / Method: vapor diffusion, hanging dropDetails: Dreyer, M.K., (1996) Acta Crystallog. sect., D52, 1082. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Oct 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→10 Å / Num. obs: 6347 / % possible obs: 95 % / Redundancy: 5.3 % / Rsym value: 0.064 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.55→2.63 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.23 / % possible all: 89 |
Reflection | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 89 % / Num. unique obs: 521 / Rmerge(I) obs: 0.023 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.55→10 Å / σ(F): 0 Details: THE 9 C-TERMINAL RESIDUES (LYS207 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS
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Refinement step | Cycle: LAST / Resolution: 2.55→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.149 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |