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Yorodumi- PDB-1cxf: COMPLEX OF A (D229N/E257Q) DOUBLE MUTANT CGTASE FROM BACILLUS CIR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cxf | |||||||||
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Title | COMPLEX OF A (D229N/E257Q) DOUBLE MUTANT CGTASE FROM BACILLUS CIRCULANS STRAIN 251 WITH MALTOTETRAOSE AT 120 K AND PH 9.1 OBTAINED AFTER SOAKING THE CRYSTAL WITH ALPHA-CYCLODEXTRIN | |||||||||
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 / Resolution: 2.1 Å | |||||||||
Authors | Knegtel, R.M.A. / Strokopytov, B.V. / Dijkstra, B.W. | |||||||||
Citation | 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. #1: 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. #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.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 Cyclomalto-Dextrin Glucanotransferase from Bacillus Circulans Authors: Lawson, C.L.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 | 1cxf.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cxf.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 1cxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cxf_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 1cxf_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 1cxf_validation.xml.gz | 31 KB | Display | |
Data in CIF | 1cxf_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/1cxf ftp://data.pdbj.org/pub/pdb/validation_reports/cx/1cxf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 372 / 2: CIS PROLINE - PRO 506 / 3: CIS PROLINE - PRO 624 / 4: CIS PROLINE - PRO 634 |
-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 / Plasmid: PDP66K- / Production host: BACILLUS CIRCULANS STRAIN DB104A 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-glucopyranose / alpha-maltotetraose |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Polysaccharide |
-Non-polymers , 2 types, 312 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.64 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.1 / Details: pH 9.1 | ||||||||||||||||||||||||||||||
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 | Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 22, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Redundancy: 2.12 % / Rmerge(I) obs: 0.054 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 40.8 Å / Num. obs: 21240 / % possible obs: 79.3 % / Num. measured all: 40543 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 2.62 Å / Lowest resolution: 2.67 Å / % possible obs: 13.1 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.286 / Highest resolution: 2.6 Å / Lowest resolution: 40.8 Å / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.5 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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