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Yorodumi- PDB-2owc: Structure of a covalent intermediate in Thermus thermophilus amyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2owc | ||||||||||||
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Title | Structure of a covalent intermediate in Thermus thermophilus amylomaltase | ||||||||||||
Components | 4-alpha-glucanotransferase | ||||||||||||
Keywords | TRANSFERASE / amylomaltase / alpha-amylase / beta-alpha-barrel / glycosyl-enzyme | ||||||||||||
Function / homology | Function and homology information 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Thermus thermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | Barends, T.R.M. / Bultema, J.B. / Kaper, T. / van der Maarel, M.J.E.C. / Dijkhuizen, L. / Dijkstra, B.W. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Three-way stabilization of the covalent intermediate in amylomaltase, an alpha-amylase-like transglycosylase. Authors: Barends, T.R. / Bultema, J.B. / Kaper, T. / van der Maarel, M.J. / Dijkhuizen, L. / Dijkstra, B.W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2owc.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2owc.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 2owc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/2owc ftp://data.pdbj.org/pub/pdb/validation_reports/ow/2owc | HTTPS FTP |
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-Related structure data
Related structure data | 2owwC 2owxC 1cwyS 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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-Components
#1: Protein | Mass: 57528.238 Da / Num. of mol.: 1 / Fragment: amylomaltase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: malq / Plasmid: pCCBmalq / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE-3) References: UniProt: Q72J82, UniProt: O87172*PLUS, 4-alpha-glucanotransferase |
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#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / acarbose-derived trisaccharide |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-MLI / |
#5: 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: 3.3 Å3/Da / Density % sol: 62.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.4-0.8 M sodium malonate pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 46013 / Num. obs: 57412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CWY Resolution: 2.05→29.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.623 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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