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Yorodumi- PDB-4s2b: Covalent complex of E. coli transaldolase TalB with tagatose-6-ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s2b | ||||||
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Title | Covalent complex of E. coli transaldolase TalB with tagatose-6-phosphate | ||||||
Components | Transaldolase BTransaldolase | ||||||
Keywords | TRANSFERASE / TIM barrel / pentose phosphate pathway / Schiff base tagatose 6-phosphate / ring sugar | ||||||
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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Stellmacher, L. / Sandalova, T. / Schneider, G. / Sprenger, G.A. / Samland, A.K. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants. Authors: Stellmacher, L. / Sandalova, T. / Schneider, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s2b.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s2b.ent.gz | 230.6 KB | Display | PDB format |
PDBx/mmJSON format | 4s2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s2b ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s2b | HTTPS FTP |
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-Related structure data
Related structure data | 4s2cC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 317 / Label seq-ID: 22 - 337
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-Components
#1: Protein | Mass: 37476.543 Da / Num. of mol.: 2 / Mutation: F178Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b0008, JW0007, talB, yaaK / Production host: Escherichia coli (E. coli) / Strain (production host): LJ110 / References: UniProt: P0A870, transaldolase #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A247T IS A NATURAL VARIANT. | |
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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: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.15 M lithium sulfate, 18% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 20, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→75.12 Å / Num. all: 140870 / Num. obs: 140870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.46→1.48 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / Num. unique all: 6871 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ONR Resolution: 1.46→75.12 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.98 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.056 / 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 max: 97.44 Å2 / Biso mean: 24.094 Å2 / Biso min: 11.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→75.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 21370 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.46→1.498 Å / Total num. of bins used: 20
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