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Yorodumi- PDB-1d3c: MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d3c | |||||||||
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Title | MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN | |||||||||
Components | CYCLODEXTRIN GLYCOSYLTRANSFERASE | |||||||||
Keywords | TRANSFERASE / ALPHA-AMYLASE / PRODUCT COMPLEX / OLIGOSACCHARIDE / FAMILY 13 GLYCOSYL HYDROLASE / TRANSGLYCOSYLATION / INDUCED FIT / CATALYSIS | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Uitdehaag, J.C.M. / Kalk, K.H. / van der Veen, B.A. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-A resolution. Authors: Uitdehaag, J.C. / Kalk, K.H. / van Der Veen, B.A. / Dijkhuizen, L. / Dijkstra, B.W. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: X-ray Structures Along the Reaction Pathway of Cyclodextrin Glycosyltransferase Elucidate Catalysis in the Alpha-amylase Family Authors: Uitdehaag, J.C.M. / Mosi, R. / Kalk, K.H. / van der Veen, B.A. / Dijkhuizen, L. / Withers, S.G. / Dijkstra, B.W. #2: Journal: J.Biol.Chem. / Year: 1995 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. #3: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d3c.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d3c.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d3c_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 1d3c_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 1d3c_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 1d3c_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3c ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3c | HTTPS FTP |
-Related structure data
Related structure data | 1cxiS 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: 74573.516 Da / Num. of mol.: 1 / Mutation: D229N, E257Q 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 , 2 types, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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#3: Polysaccharide |
-Non-polymers , 3 types, 643 molecules
#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THIS IS THE STRUCTURE OF B. CIRCULANS 251 E257Q/D229N CGTASE WITH GAMMA-CYCLODEXTR |
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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: 2.8 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.3 Details: 60 % MPD, 100 MM TRIS PH 8.1, pH 10.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.55 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.908 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→80 Å / Num. all: 80898 / Num. obs: 78720 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4 / Redundancy: 5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.6 / % possible all: 71 |
Reflection shell | *PLUS % possible obs: 71 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXI Resolution: 1.78→8 Å / Isotropic thermal model: TNT STANDARD LIBRARY / Cross valid method: RFREE / σ(F): 0 / σ(I): 0 Stereochemistry target values: ENGH & HUBER; GAMMA CD FROM HARATA, CHEM. LETT 1984, PP 641-644
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 202.89 Å2 / ksol: 0.87884 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→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 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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