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Yorodumi- PDB-1dtu: BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE: A... -
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-Basic information
Entry | Database: PDB / ID: 1dtu | ||||||||||||
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Title | BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE: A MUTANT Y89D/S146P COMPLEXED TO AN HEXASACCHARIDE INHIBITOR | ||||||||||||
Components | PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE) | ||||||||||||
Keywords | TRANSFERASE / ALPHA-AMYLASE / ACARBOSE / INHIBITOR COMPLEX / FAMILY 13 GLYCOSYL HYDROLASE / MUTANT / PRODUCT SPECIFICITY / CYCLODEXTRIN | ||||||||||||
Function / homology | Function and homology information cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Bacillus circulans (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Uitdehaag, J.C.M. / Kalk, K.H. / Dijkstra, B.W. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Rational design of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 to increase alpha-cyclodextrin production. Authors: van der Veen, B.A. / Uitdehaag, J.C. / Penninga, D. / van Alebeek, G.J. / Smith, L.M. / Dijkstra, B.W. / Dijkhuizen, L. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 Authors: Wind, R.D. / Uitdehaag, J.C.M. / Buitelaar, R.M. / Dijkstra, B.W. / Dijkhuizen, L. #2: Journal: Biochemistry / Year: 1996 Title: Structure of Cyclodextrin Glycosyltransferase Complexed with a Maltononaose Inhibitor at 2.6 Angstrom Resolution. Implications for Product Specificity Authors: Strokopytov, B. / Knegtel, R.M. / Penninga, D. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W. #3: Journal: Biochemistry / Year: 1995 Title: Site Directed Mutagenesis in Tyrosine 195 of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 Affect Activity and Product Specificity Authors: Penninga, D. / Strokopytov, B. / Rozeboom, H.J. / Lawson, C.L. / Dijkstra, B.W. / Bergsma, J. / Dijkhuizen, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtu.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtu.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtu ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtu | HTTPS FTP |
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-Related structure data
Related structure data | 1cxg 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74537.430 Da / Num. of mol.: 1 / Mutation: Y89D, S146P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251 / Cellular location: EXTRACELLULAR / Plasmid: PDP66S / Production host: Bacillus subtilis (bacteria) References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
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#3: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | #5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 276 molecules
#6: Chemical | #7: Chemical | ChemComp-ADH / | #8: 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: 2.94 Å3/Da / Density % sol: 58.2 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 60 % MPD, 100 MM TRIS PH 7.1, 5% (w/v) maltose, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.86 Å / Num. all: 35279 / Num. obs: 32700 / % possible obs: 92.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.0747 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.256 / Num. unique all: 1574 / % possible all: 88.8 |
Reflection | *PLUS Num. measured all: 126519 |
Reflection shell | *PLUS % possible obs: 88.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXG 1cxg Resolution: 2.4→8 Å / Isotropic thermal model: TNT STANDARD LIBRARY / Cross valid method: RFREE / σ(F): 0 / σ(I): 0 Stereochemistry target values: TNT STANDARD LIBRARY (pre-PRIESTLE VERSION) Details: Stereochemistry targets in general correspond to Engh&Huber The electron density imposes non-ideal stereochemistry of the C1-N1 bond and C5 coordination of acarviosine in subsite -1. This ...Details: Stereochemistry targets in general correspond to Engh&Huber The electron density imposes non-ideal stereochemistry of the C1-N1 bond and C5 coordination of acarviosine in subsite -1. This might reflect presence of multiple chemical species. The resolution is too low to resolve this. The side-chain of residue Arg 47 was modelled in 2 conformations with 50% occupancy each.
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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