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Yorodumi- PDB-1eo5: Bacillus circulans strain 251 cyclodextrin glycosyltransferase in... -
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-Basic information
Entry | Database: PDB / ID: 1eo5 | |||||||||
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Title | Bacillus circulans strain 251 cyclodextrin glycosyltransferase in complex with maltoheptaose | |||||||||
Components | PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE) | |||||||||
Keywords | TRANSFERASE / ALPHA-AMYLASE / MALTOHEPTAOSE / 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: 2 Å | |||||||||
Authors | Uitdehaag, J.C.M. / Dijkstra, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structures of maltohexaose and maltoheptaose bound at the donor sites of cyclodextrin glycosyltransferase give insight into the mechanisms of transglycosylation activity and cyclodextrin size specificity. Authors: Uitdehaag, J.C. / van Alebeek, G.J. / van Der Veen, B.A. / Dijkhuizen, L. / Dijkstra, B.W. #1: 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 Angstrom Resolution Authors: Uitdehaag, J.C.M. / Kalk, K.H. / Van Der Veen, B.A. / Dijkhuizen, L. / Dijkstra, B.W. #2: 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. #3: 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.A. / Strokopytov, B. / Penninga, D. / Faber, O.G. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W. #4: 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.A. / 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 | 1eo5.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eo5.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 1eo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eo5_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1eo5_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1eo5_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 1eo5_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/1eo5 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/1eo5 | HTTPS FTP |
-Related structure data
Related structure data | 1eo7C 1cxiS S: Starting model for refinement C: citing same article (ref.) |
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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: 74457.375 Da / Num. of mol.: 1 / Mutation: E257A,D229A 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 , 3 types, 4 molecules
#2: 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)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose | |
-Non-polymers , 3 types, 678 molecules
#5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THIS IS THE STRUCTURE OF B. CIRCULANS 251 E257A/D229A CGTASE WITH MALTOHEPTA |
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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: 2.9 Å3/Da / Density % sol: 57.4 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.1 Details: 60% MPD, 100 mM Tris, 5% maltose, pH 6.10, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS pH: 8.1 / Method: vapor diffusion / Details: Lawson, C.L., (1994) J. Mol. Biol., 236, 590. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9063 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9063 Å / Relative weight: 1 |
Reflection | Resolution: 2→79.9 Å / Num. all: 59419 / Num. obs: 54766 / % possible obs: 92.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.48 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 7.72 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.414 / % possible all: 88.1 |
Reflection shell | *PLUS % possible obs: 88.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXI Resolution: 2→8 Å / Isotropic thermal model: TNT STANDARD LIBRARY / Cross valid method: RFREE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: for sugar restraints see related entries
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 231.6 Å2 / ksol: 0.773 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.169 / Rfactor obs: 0.167 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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