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Yorodumi- PDB-1cxl: COMPLEX BETWEEN A COVALENT INTERMEDIATE AND BACILLUS CIRCULANS ST... -
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-Basic information
Entry | Database: PDB / ID: 1cxl | |||||||||
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Title | COMPLEX BETWEEN A COVALENT INTERMEDIATE AND BACILLUS CIRCULANS STRAIN 251 CGTASE E257Q | |||||||||
Components | PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE) | |||||||||
Keywords | GLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE FAMILY 13 / ALPHA-AMYLASE FAMILY / INTERMEDIATE COMPLEX / 4- DEOXYMALTOTRIOSE | |||||||||
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: 1.81 Å | |||||||||
Authors | Uitdehaag, J.C.M. / Dijkstra, B.W. | |||||||||
Citation | 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. / Mosi, R. / Kalk, K.H. / van der Veen, B.A. / Dijkhuizen, L. / Withers, S.G. / 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. / Ruiterkamp, R. / Dijkstra, B.W. / Withers, S.G. #2: 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. #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. / Strokopytov, B. / Penninga, D. / Faber, O.G. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W. #4: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cxl.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cxl.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/1cxl ftp://data.pdbj.org/pub/pdb/validation_reports/cx/1cxl | HTTPS FTP |
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-Related structure data
Related structure data | 1cxkC 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: 74558.438 Da / Num. of mol.: 1 / Mutation: E257Q Source method: isolated from a genetically manipulated source Details: COVALENTLY BOUND REACTION INTERMEDIATE / Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251 Description: MUTANTS WERE CONSTRUCTED IN ECOLI STRAIN MC1061 Plasmid: PDP66S / Gene (production host): CGT / Production host: Bacillus subtilis (bacteria) / Strain (production host): DB104A References: UniProt: CDGU_BACCI, UniProt: P43379*PLUS, cyclomaltodextrin glucanotransferase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 672 molecules
#5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE ...CA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE PREVIOUS RESIDUE VIA AN ALPHA(1->4) GLYCOSIDIC |
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Sequence details | SER 400 AFTER REINTERPRE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % Description: ELECTRON DENSITY AT SUBSITES +1 AND +2 IS AMBIGUOUS, THREE WATER MOLECULES WERE PLACED THERE TO REPRESENT THIS DENSITY | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 Details: CRYSTAL SOAKED FIRST IN 4-DEOXY MALTOSE,THEN IN 4-DEOXY MALTOTRIOSYL ALPHA- FLUORIDE, pH 6.10 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion / Details: Lawson, C.L., (1990) J.Mol.Biol., 214, 807. | ||||||||||||||||||||||||||||||
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: BW7B / Wavelength: 0.8838 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8838 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→58.54 Å / Num. obs: 73264 / % possible obs: 94.9 % / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 17.51 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3 / % possible all: 49.9 |
Reflection | *PLUS % possible obs: 94.9 % |
Reflection shell | *PLUS Highest resolution: 1.81 Å / Lowest resolution: 1.83 Å / % possible obs: 49.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXI Resolution: 1.81→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 216.9 Å2 / ksol: 0.774 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.81 Å / Lowest resolution: 8 Å / Rfactor obs: 0.155 / Rfactor Rfree: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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