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- PDB-1dtu: BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE: A... -

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Basic information

Entry
Database: PDB / ID: 1dtu
TitleBACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE: A MUTANT Y89D/S146P COMPLEXED TO AN HEXASACCHARIDE INHIBITOR
ComponentsPROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)
KeywordsTRANSFERASE / ALPHA-AMYLASE / ACARBOSE / INHIBITOR COMPLEX / FAMILY 13 GLYCOSYL HYDROLASE / MUTANT / PRODUCT SPECIFICITY / CYCLODEXTRIN
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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / alpha-maltotriose / Chem-ADH / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUitdehaag, J.C.M. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Rational design of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 to increase alpha-cyclodextrin production.
Authors: van der Veen, B.A. / Uitdehaag, J.C. / Penninga, D. / van Alebeek, G.J. / Smith, L.M. / Dijkstra, B.W. / Dijkhuizen, L.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1
Authors: Wind, R.D. / Uitdehaag, J.C.M. / Buitelaar, R.M. / Dijkstra, B.W. / Dijkhuizen, L.
#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: Biochemistry / Year: 1995
Title: Site Directed Mutagenesis in Tyrosine 195 of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 Affect Activity and Product Specificity
Authors: Penninga, D. / Strokopytov, B. / Rozeboom, H.J. / Lawson, C.L. / Dijkstra, B.W. / Bergsma, J. / Dijkhuizen, L.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2017Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _struct_conn.ptnr1_label_atom_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_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 / _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.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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 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 3.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)77,2839
Polymers74,5371
Non-polymers2,7468
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.445, 111.160, 65.758
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: 74537.430 Da / Num. of mol.: 1 / Mutation: Y89D, S146P
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 , 4 types, 5 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 alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-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.: 2
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
#5: 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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 276 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-ADH / 1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE


Mass: 159.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 60 % MPD, 100 MM TRIS PH 7.1, 5% (w/v) maltose, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 %(v/v)MPD1reservoir
2100 mMHEPES1reservoir
35 %(w/v)maltose1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→28.86 Å / Num. all: 35279 / Num. obs: 32700 / % possible obs: 92.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.0747 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.256 / Num. unique all: 1574 / % possible all: 88.8
Reflection
*PLUS
Num. measured all: 126519
Reflection shell
*PLUS
% possible obs: 88.8 %

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Processing

Software
NameClassification
XDSdata scaling
BIOMOLdata reduction
TNTrefinement
XDSdata reduction
BIOMOLdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXG

1cxg
PDB Unreleased entry


Resolution: 2.4→8 Å / Isotropic thermal model: TNT STANDARD LIBRARY / Cross valid method: RFREE / σ(F): 0 / σ(I): 0
Stereochemistry target values: TNT STANDARD LIBRARY (pre-PRIESTLE VERSION)
Details: Stereochemistry targets in general correspond to Engh&Huber The electron density imposes non-ideal stereochemistry of the C1-N1 bond and C5 coordination of acarviosine in subsite -1. This ...Details: Stereochemistry targets in general correspond to Engh&Huber The electron density imposes non-ideal stereochemistry of the C1-N1 bond and C5 coordination of acarviosine in subsite -1. This might reflect presence of multiple chemical species. The resolution is too low to resolve this. The side-chain of residue Arg 47 was modelled in 2 conformations with 50% occupancy each.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2171 6 %RANDOM
Rwork0.206 ---
all0.209 32641 --
obs0.209 32700 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 181 273 5722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.0025591
X-RAY DIFFRACTIONt_angle_deg1.157617
X-RAY DIFFRACTIONt_dihedral_angle_d17.1353136
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.002148
X-RAY DIFFRACTIONt_gen_planes0.01796
X-RAY DIFFRACTIONt_it1.4135588
X-RAY DIFFRACTIONt_nbd0.009287
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.135
X-RAY DIFFRACTIONt_plane_restr0.01

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