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- PDB-1eo7: BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE IN... -

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Basic information

Entry
Database: PDB / ID: 1eo7
TitleBACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE IN COMPLEX WITH MALTOHEXAOSE
ComponentsPROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)
KeywordsTRANSFERASE / ALPHA-AMYLASE / MALTOHEXAOSE / OLIGOSACCHARIDE / FAMILY 13 GLYCOSYL HYDROLASE / TRANSGLYCOSYLATION / INDUCED FIT / CATALYSIS / CYCLODEXTRIN
Function / homologyGlycosyl hydrolase, all-beta / Alpha-amylase, C-terminal domain / CBM20 (carbohydrate binding type-20) domain profile. / Alpha amylase, C-terminal all-beta domain / IPT/TIG domain / Starch binding domain / Carbohydrate binding module family 20 / IPT domain / Alpha amylase / Glycosyl hydrolase, family 13, catalytic domain ...Glycosyl hydrolase, all-beta / Alpha-amylase, C-terminal domain / CBM20 (carbohydrate binding type-20) domain profile. / Alpha amylase, C-terminal all-beta domain / IPT/TIG domain / Starch binding domain / Carbohydrate binding module family 20 / IPT domain / Alpha amylase / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, catalytic domain / Immunoglobulin-like fold / Carbohydrate-binding-like fold / Immunoglobulin E-set / Glycoside hydrolase superfamily / cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / carbohydrate metabolic process / extracellular region / metal ion binding / Cyclomaltodextrin glucanotransferase
Function and homology information
Specimen sourceBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.48 Å resolution
AuthorsUitdehaag, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2000 / Release: Nov 22, 2000
RevisionDateData content typeGroupProviderType
1.0Nov 22, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,46020
Polyers74,4571
Non-polymers3,00319
Water2,612145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)111.648, 109.022, 64.677
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)


Mass: 74457.375 Da / Num. of mol.: 1 / Mutation: E257A/D229A / Source: (gene. exp.) Bacillus circulans (bacteria) / Genus: Bacillus / Strain: 251 / Cellular location: EXTRACELLULAR / Plasmid name: PDP66S / Genus (production host): Bacillus / Production host: Bacillus subtilis (bacteria)
References: UniProt: P43379, cyclomaltodextrin glucanotransferase
#2: Chemical
ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 16 / Formula: C6H12O6 / Glucose
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca / Calcium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Formula: H2O / Water
Compound detailsTHIS IS THE STRUCTURE OF B. CIRCULANS 251 E257A/D229A CGTASE WITH MALTOHEPTAOSE IN ITS ACTIVE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 / Density percent sol: 53.2 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 60% MPD, 100 mM Tris, 5% w/v maltose, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.1 / Method: vapor diffusion / Details: Lawson, C.L., (1994) J. Mol. Biol., 236, 590.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
160 %(v/v)MPD1reservoir
2100 mMTris-HCl1reservoir
35 %(w/v)maltose1reservoir

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Data collection

DiffractionMean temperature: 12 kelvins
SourceSource: SYNCHROTRON / Type: ELETTRA BEAMLINE 5.2R / Synchrotron site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0001
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jul 14, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 19.1 Å2 / D resolution high: 2.48 Å / D resolution low: 78 Å / Number all: 28669 / Number obs: 26146 / Observed criterion sigma F: 4 / Observed criterion sigma I: 4 / Rmerge I obs: 0.061 / Rsym value: 0.061 / NetI over sigmaI: 14.36 / Redundancy: 3.27 % / Percent possible obs: 91.2
Reflection shellRmerge I obs: 0.225 / Highest resolution: 2.49 Å / Lowest resolution: 2.55 Å / MeanI over sigI obs: 4.2 / Number unique all: 1604 / Rsym value: 0.225 / Redundancy: 2.7 % / Percent possible all: 86.4
Reflection shell
*PLUS
Percent possible obs: 86.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXL
Details: for sugar restraints see related entries / R Free selection details: RANDOM / Isotropic thermal model: TNT STANDARD LIBRARY / Cross valid method: RFREE / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: ENGH & HUBER
Solvent computationSolvent model details: BABINET SCALING / Solvent model param bsol: 117.9 / Solvent model param ksol: 0.935
Least-squares processR factor R free: 0.296 / R factor R work: 0.228 / R factor all: 0.231 / R factor obs: 0.231 / Highest resolution: 2.48 Å / Lowest resolution: 7 Å / Number reflection R free: 1461 / Number reflection all: 24736 / Number reflection obs: 24736 / Percent reflection R free: 5.9 / Percent reflection obs: 91
Refine hist #LASTHighest resolution: 2.48 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 5257 / Nucleic acid: 0 / Ligand: 183 / Solvent: 145 / Total: 5585
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00655804.000
X-RAY DIFFRACTIONt_angle_deg0.719760210.000
X-RAY DIFFRACTIONt_dihedral_angle_d18.51031270.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0.000
X-RAY DIFFRACTIONt_trig_c_planes0.0061458.000
X-RAY DIFFRACTIONt_gen_planes0.00779530.000
X-RAY DIFFRACTIONt_it1.03255765.000
X-RAY DIFFRACTIONt_nbd0.012273100.000
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.228 / R factor all: 0.231 / R factor obs: 0.228
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0068.000
X-RAY DIFFRACTIONt_plane_restr0.00730.000

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