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Yorodumi- PDB-2cxg: CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED TO THE INHIBITOR ACARBOSE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cxg | |||||||||||||||
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Title | CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED TO THE INHIBITOR ACARBOSE | |||||||||||||||
Components | CYCLODEXTRIN GLYCOSYLTRANSFERASE | |||||||||||||||
Keywords | GLYCOSYLTRANSFERASE | |||||||||||||||
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: 2.5 Å | |||||||||||||||
Authors | Strokopytov, B.V. / Uitdehaag, J.C.M. / Ruiterkamp, R. / Dijkstra, B.W. | |||||||||||||||
Citation | 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. #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: 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. #3: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cxg.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cxg.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cxg ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cxg | HTTPS FTP |
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-Related structure data
Related structure data | 1cdgS 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: 74575.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEXED TO AN ACARBOSE-DERIVED MALTOTETRAOSE INHIBITOR Source: (natural) Bacillus circulans (bacteria) / Strain: 251 References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | #3: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose | #6: Sugar | ChemComp-GLC / | |
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-Non-polymers , 3 types, 95 molecules
#5: Chemical | ChemComp-ACI / | ||
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#7: Chemical | #8: 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: 2.9 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.55 Details: PROTEIN WAS CRYSTALLIZED FROM OTHER LIQUOR CONTAINING 60% V/V METHYL-PENTANEDIOL (MPD) 100 MM SODIUM-HEPES PH 7.55 AND 0.5% W/V MALTOSE THEN SOAKED IN MOTHER LIQUOR WITH 0.1 % ACARBOSE AND 0. ...Details: PROTEIN WAS CRYSTALLIZED FROM OTHER LIQUOR CONTAINING 60% V/V METHYL-PENTANEDIOL (MPD) 100 MM SODIUM-HEPES PH 7.55 AND 0.5% W/V MALTOSE THEN SOAKED IN MOTHER LIQUOR WITH 0.1 % ACARBOSE AND 0.5 % MALTOSE FOR 5 DAYS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 1, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29 Å / Num. obs: 59552 / % possible obs: 73.9 % / Observed criterion σ(I): 0 / Redundancy: 2.42 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 |
Reflection shell | Resolution: 2.5→2.58 Å / % possible all: 40.3 |
Reflection shell | *PLUS % possible obs: 40.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CDG Resolution: 2.5→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE / 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
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 248.5 Å2 / ksol: 0.891 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.007 / Weight: 30 |