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- PDB-1eo5: Bacillus circulans strain 251 cyclodextrin glycosyltransferase in... -

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Basic information

Entry
Database: PDB / ID: 1eo5
TitleBacillus circulans strain 251 cyclodextrin glycosyltransferase in complex with maltoheptaose
ComponentsPROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)
KeywordsTRANSFERASE / ALPHA-AMYLASE / MALTOHEPTAOSE / OLIGOSACCHARIDE / FAMILY 13 GLYCOSYL HYDROLASE / TRANSGLYCOSYLATION / INDUCED FIT / CATALYSIS
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase activity / cyclomaltodextrin glucanotransferase / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Starch binding domain / Carbohydrate binding module family 20 / 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 ...CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Starch binding domain / Carbohydrate binding module family 20 / 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 / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / alpha-maltotetraose / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
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.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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_conn_type / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_type.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6869
Polymers74,4571
Non-polymers3,2298
Water12,142674
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.700, 109.700, 67.500
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 PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)


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: EXTRACELLULARGlossary of biology / 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


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 678 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.4 %
Crystal growMethod: 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
IDConc.Common nameCrystal-IDSol-ID
160 %(v/v)MPD1reservoir
2100 mMTris-HCl1reservoir
35 %(w/v)maltose1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9063
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9063 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2469 4.9 %RANDOM
Rwork0.167 ---
all0.169 50660 --
obs0.169 50660 87 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 231.6 Å2 / ksol: 0.773 e/Å3
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 213 674 6144
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00656114
X-RAY DIFFRACTIONt_angle_deg0.652764810
X-RAY DIFFRACTIONt_dihedral_angle_d16.90531270
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.0051458
X-RAY DIFFRACTIONt_gen_planes0.01679530
X-RAY DIFFRACTIONt_it1.45756075
X-RAY DIFFRACTIONt_nbd0.01139450
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
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0058
X-RAY DIFFRACTIONt_plane_restr0.01630

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