[English] 日本語
Yorodumi- PDB-2dij: COMPLEX OF A Y195F MUTANT CGTASE FROM B. CIRCULANS STRAIN 251 COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dij | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | COMPLEX OF A Y195F MUTANT CGTASE FROM B. CIRCULANS STRAIN 251 COMPLEXED WITH A MALTONONAOSE INHIBITOR AT PH 9.8 OBTAINED AFTER SOAKING THE CRYSTAL WITH ACARBOSE AND MALTOHEXAOSE | |||||||||||||||
Components | CYCLODEXTRIN GLYCOSYLTRANSFERASE | |||||||||||||||
Keywords | GLYCOSYLTRANSFERASE / TRANSFERASE | |||||||||||||||
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: 2.6 Å | |||||||||||||||
Authors | Strokopytov, B.V. / Knegtel, R.M.A. / Uitdehaag, J.C.M. / Dijkstra, B.W. | |||||||||||||||
Citation | 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. #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.M. / Ruiterkamp, R. / Dijkstra, B.W. / Withers, S.G. #2: Journal: To be Published Title: Kinetic Evidence that Acarbose is a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase Authors: Mosi, R. / Sham, H. / Uitdehaag, J.C.M. / Ruiterkamp, R. / Dijkstra, B.W. / Withers, S.G. #3: Journal: Biochemistry / Year: 1995 Title: X-Ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose. Implications for the Catalytic Mechanism of Glycosidases Authors: Strokopytov, B. / Penninga, D. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W. #4: Journal: Biochemistry / Year: 1995 Title: Site-Directed Mutations 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. #5: Journal: J.Mol.Biol. / Year: 1994 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. #6: Journal: J.Mol.Biol. / Year: 1990 Title: Maltodextrin-Dependent Crystallization of Cyclomaltodextrin Glucanotransferase from Bacillus Circulans Authors: Lawson, C.L. / Bergsma, J. / Bruinenberg, P.M. / De Vries, G. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dij.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dij.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dij_validation.pdf.gz | 689.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2dij_full_validation.pdf.gz | 711.1 KB | Display | |
Data in XML | 2dij_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2dij_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/2dij ftp://data.pdbj.org/pub/pdb/validation_reports/di/2dij | HTTPS FTP |
-Related structure data
Related structure data | 1dij S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74559.484 Da / Num. of mol.: 1 / Mutation: Y195F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251 Description: MUTANTS OF BACILLUS CIRCULANS STRAIN 251 CGTASE WERE CONSTRUCTED IN E. COLI AND AFTERWARDS EXPRESSED ON PLASMID PDP66S TRANSFORMED TO B. SUBTILIS STRAIN DB104A Plasmid: PDP66S / Production host: Escherichia coli (E. coli) References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
---|
-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
---|---|
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#4: 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 / alpha-maltopentaose |
#5: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: 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 / alpha-maltohexaose |
-Non-polymers , 3 types, 129 molecules
#7: Chemical | #8: Chemical | ChemComp-ADH / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 9.8 / Details: SOAKED WITH ACARBOSE AND MALTOHEXAOSE, pH 9.8 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→28.19 Å / Num. obs: 27013 / % possible obs: 94.1 % / Observed criterion σ(I): 2.2 / Redundancy: 2.81 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / % possible all: 71.1 |
Reflection | *PLUS Num. measured all: 79898 |
Reflection shell | *PLUS % possible obs: 71.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DIJ 1dij Resolution: 2.6→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: IDEAL PARAMETERS FOR GLUCOSE FROM TAKUSAGAWA & JACOBSON (1978), ACTA CRYST. B34:213-218, FOR ACARBOSE FROM STROKOPYTOV ET AL. (1995) BIOCHEMISTRY 34:2234-2240
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET SCALING / Bsol: 131.1 Å2 / ksol: 0.756 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 2701 % / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.007 / Weight: 30 |