+Open data
-Basic information
Entry | Database: PDB / ID: 1l6w | ||||||
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Title | Fructose-6-phosphate aldolase | ||||||
Components | Fructose-6-phosphate aldolase 1 | ||||||
Keywords | LYASE / alpha-beta barrel / domain swapping | ||||||
Function / homology | Function and homology information ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.93 Å | ||||||
Authors | Thorell, S. / Schuermann, M. / Sprenger, G.A. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of decameric fructose-6-phosphate aldolase from Escherichia coli reveals inter-subunit helix swapping as a structural basis for assembly differences in the transaldolase family. Authors: Thorell, S. / Schurmann, M. / Sprenger, G.A. / Schneider, G. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Fructose-6-phosphate Aldolase Is a Novel Class I Aldolase from Escherichia coli and Is Related to a Novel Group of Bacterial Transaldolases Authors: Schuermann, M. / Sprenger, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l6w.cif.gz | 422.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6w.ent.gz | 357 KB | Display | PDB format |
PDBx/mmJSON format | 1l6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l6w_validation.pdf.gz | 511 KB | Display | wwPDB validaton report |
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Full document | 1l6w_full_validation.pdf.gz | 537.4 KB | Display | |
Data in XML | 1l6w_validation.xml.gz | 92.6 KB | Display | |
Data in CIF | 1l6w_validation.cif.gz | 128.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6w ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6w | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 23016.756 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fsa / Plasmid: pUC18fsa / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 107 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.93→19.94 Å / Num. all: 200850 / Num. obs: 200177 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 11.3 Å2 / Limit h max: 59 / Limit h min: 0 / Limit k max: 65 / Limit k min: 0 / Limit l max: 95 / Limit l min: 0 / Observed criterion F max: 3950506.21 / Observed criterion F min: 11 / Rmerge(I) obs: 0.038 / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.93→1.96 Å / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 18 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 200850 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 18 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 1.93→19.94 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 60.0517 Å2 / ksol: 0.412232 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.2 Å2 / Biso mean: 18.93 Å2 / Biso min: 6.63 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→19.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.006 / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.199 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.231 / Rfactor Rwork: 0.202 / Rfactor obs: 0.202 |