+Open data
-Basic information
Entry | Database: PDB / ID: 2owx | |||||||||
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Title | THERMUS THERMOPHILUS AMYLOMALTASE AT pH 5.6 | |||||||||
Components | 4-alpha-glucanotransferase | |||||||||
Keywords | TRANSFERASE / BETA-ALPHA-8 BARREL / SUCCINIMIDE RESIDUE IN MAIN CHAIN | |||||||||
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: 2.5 Å | |||||||||
Authors | Barends, T.R.M. / Kaper, T. / Bultema, J.J. / Dijkhuizen, L. / van der Maarel, J.E.C. / 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 | 2owx.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2owx.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 2owx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/2owx ftp://data.pdbj.org/pub/pdb/validation_reports/ow/2owx | HTTPS FTP |
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-Related structure data
Related structure data | 2owcC 2owwC 1cwyS C: citing same article (ref.) S: Starting model for refinement |
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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: SEQUENCE DATABASE RESIDUES 21-500 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: Chemical | ChemComp-MLI / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 3.6 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: SODIUM MALONATE, PH 5.6, 1 mM DTT, pH 5.60, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.83 / Wavelength: 0.83 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 22, 2004 / Details: PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR | |||||||||
Radiation | Monochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→99 Å / Num. obs: 25247 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9 | |||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.4 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CWY Resolution: 2.5→34.92 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.304 / 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 mean: 45.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.569 Å / Total num. of bins used: 20
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