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- PDB-1d3c: MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN G... -

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Basic information

Entry
Database: PDB / ID: 1d3c
TitleMICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / 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
Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase ...Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / IPT/TIG domain / IPT domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / gamma-cyclodextrin / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsUitdehaag, 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
DepositionSep 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1009
Polymers74,5741
Non-polymers4,5268
Water11,512639
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.791, 109.532, 65.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYCLODEXTRIN GLYCOSYLTRANSFERASE


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


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide Cyclooctakis-(1-4)-(alpha-D-glucopyranose) / gamma-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: gamma-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,8,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a1-h4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0

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Non-polymers , 3 types, 643 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS IS THE STRUCTURE OF B. CIRCULANS 251 E257Q/D229N CGTASE WITH GAMMA-CYCLODEXTRIN 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
160 %(v/v)MPD11
2100 mMHEPES11
35.0 %(w/v)maltose11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.908
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXI

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
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3984 5 %RANDOM
Rwork0.22 ---
all0.222 78720 --
obs0.222 78720 97.7 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 202.89 Å2 / ksol: 0.87884 e/Å3
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 290 647 6201
Refine LS restraints
Refine-IDTypeDev idealNumberDev ideal target
X-RAY DIFFRACTIONt_bond_d0.0065714
X-RAY DIFFRACTIONt_angle_deg0.7357804
X-RAY DIFFRACTIONt_dihedral_angle_d17.0833132
X-RAY DIFFRACTIONt_trig_c_planes0.007147
X-RAY DIFFRACTIONt_gen_planes0.011795
X-RAY DIFFRACTIONt_it1.5185714
X-RAY DIFFRACTIONt_nbd0.011449
X-RAY DIFFRACTIONt_incorr_chiral_ct000
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.083
X-RAY DIFFRACTIONt_plane_restr0.011

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