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Yorodumi- PDB-1i2o: CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT E96A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i2o | ||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT E96A | ||||||
Components | TRANSALDOLASE B | ||||||
Keywords | TRANSFERASE / alpha-beta barrel | ||||||
Function / homology | Function and homology information transketolase or transaldolase activity / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Thorell, S. / Jia, J. / Schneider, G. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Identification of catalytically important residues in the active site of Escherichia coli transaldolase. Authors: Schorken, U. / Thorell, S. / Schurmann, M. / Jia, J. / Sprenger, G.A. / Schneider, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-ray Analysis of Recombinant Transaldolase B from Escherichia coli Authors: Jia, J. / Lindqvist, Y. / Schneider, G. / Schoerken, U. / Sahm, H. / Sprenger, G.A. #2: Journal: Structure / Year: 1996 Title: Crystal Structure of Transaldolase B from Escherichia coli Suggests a Circular Permutation of the Alpha/beta Barrel Within the Class I Aldolase Family Authors: Jia, J. / Huang, W. / Schoerken, U. / Sahm, H. / Sprenger, G.A. / Lindqvist, Y. / Schneider, G. #3: Journal: Protein Sci. / Year: 1997 Title: Crystal Structure of the Reduced Schiff-base Intermediate Complex of Transaldolase B from Escherichia coli: Mechanistic Implications for Class I Aldolases Authors: Jia, J. / Schoerken, U. / Lindqvist, Y. / Sprenger, G.A. / Schneider, G. #4: Journal: FEBS Lett. / Year: 2000 Title: The Three-dimensional Structure of Human Transaldolase Authors: Thorell, S. / Gergely Jr., P. / Banki, K. / Perl, A. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i2o.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i2o.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 1i2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/1i2o ftp://data.pdbj.org/pub/pdb/validation_reports/i2/1i2o | HTTPS FTP |
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-Related structure data
Related structure data | 1i2nC 1i2pC 1i2qC 1i2rC 1onrS S: Starting model for refinement 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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Details | The dimer is generated with a symmetry molecule from one of the monomers in the asymmetric unit. |
-Components
#1: Protein | Mass: 35069.926 Da / Num. of mol.: 2 / Mutation: E96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TALB / Plasmid: PGSJ451 / Production host: Escherichia coli (E. coli) / Strain (production host): LJ110 / References: UniProt: P0A870, transaldolase #2: 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: 2.97 Å3/Da / Density % sol: 58.57 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 6000, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding, Jia, J., (1996) Acta Crystallogr., Sect.D, 52, 192. | ||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 1997 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. all: 49388 / Num. obs: 49388 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.05→2.1 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2994 / % possible all: 86.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 237049 |
Reflection shell | *PLUS % possible obs: 86.1 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1ONR Resolution: 2.05→19.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2164303.47 / Data cutoff low absF: 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: FLAT MODEL / Bsol: 52.63 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.5 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.236 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.223 / Rfactor obs: 0.248 |