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- PDB-1cxk: COMPLEX BETWEEN A MALTONONAOSE SUBSTRATE AND BACILLUS CIRCULANS S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cxk | |||||||||
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Title | COMPLEX BETWEEN A MALTONONAOSE SUBSTRATE AND BACILLUS CIRCULANS STRAIN 251 CGTASE E257Q/D229N | |||||||||
![]() | PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE) | |||||||||
![]() | TRANSFERASE / GLYCOSYL HYDROLASE FAMILY 13 / ALPHA-AMYLASE FAMILY / SUBSTRATE COMPLEX / MALTONONAOSE | |||||||||
Function / homology | ![]() cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Uitdehaag, J.C.M. / Kalk, K.H. / Dijkstra, B.W. | |||||||||
![]() | ![]() Title: X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Authors: Uitdehaag, J.C. / Mosi, R. / Kalk, K.H. / van der Veen, B.A. / Dijkhuizen, L. / Withers, S.G. / Dijkstra, B.W. #1: Journal: Biochemistry / Year: 1998 Title: Reassessment of acarbose as a transition state analogue inhibitor of cyclodextrin glycosyltransferase. Authors: Mosi, R. / Sham, H. / Uitdehaag, J.C. / Ruiterkamp, R. / Dijkstra, B.W. / Withers, S.G. #2: ![]() 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: ![]() Title: Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products. Authors: Knegtel, R.M. / Strokopytov, B. / Penninga, D. / Faber, O.G. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W. #4: ![]() Title: Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. Authors: Lawson, C.L. / van Montfort, R. / Strokopytov, B. / Rozeboom, H.J. / Kalk, K.H. / de Vries, G.E. / Penninga, D. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 600.7 KB | Display | ![]() |
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Full document | ![]() | 613.2 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cxlC ![]() 1cxiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 74573.516 Da / Num. of mol.: 1 / Mutation: E257Q, D229N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: MUTANTS WERE CONSTRUCTED IN ECOLI STRAIN MC1061 Plasmid: PDP66S / Gene (production host): CGT / Production host: ![]() ![]() References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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#3: 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide |
-Non-polymers , 2 types, 635 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE ...CA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE PREVIOUS RESIDUE VIA AN ALPHA(1->4) GLYCOSIDIC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 61 % Description: STEREOCHEMICAL RESTRAINTS ON SUGAR IN SUBSITE -1 WERE 10X RELAXED COMPARED TO OTHER SUGARS | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 10.3 / Details: pH 10.30 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1996 |
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: 2.09→22.92 Å / Num. obs: 45159 / % possible obs: 84.9 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.16 / % possible all: 27.6 |
Reflection | *PLUS % possible obs: 84.9 % |
Reflection shell | *PLUS % possible obs: 27.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CXI Resolution: 2.09→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 206.4 Å2 / ksol: 0.737 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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