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- PDB-3cgt: STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS ... -

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Basic information

Entry
Database: PDB / ID: 3cgt
TitleSTRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS MAIN PRODUCT BETA-CYCLODEXTRIN
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsGLYCOSYLTRANSFERASE / STARCH DEGRADATION / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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
beta-cyclodextrin / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsSchmidt, A.K. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 1998
Title: Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
Authors: Schmidt, A.K. / Cottaz, S. / Driguez, H. / Schulz, G.E.
#1: Journal: Biochemistry / Year: 1992
Title: Catalytic Center of Cyclodextrin Glycosyltransferase Derived from X-Ray Structure Analysis Combined with Site-Directed Mutagenesis
Authors: Klein, C. / Hollender, J. / Bender, H. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Cyclodextrin Glycosyltransferase Refined at 2.0 A Resolution
Authors: Klein, C. / Schulz, G.E.
#3: Journal: Appl.Microbiol.Biotechnol. / Year: 1990
Title: Molecular Cloning, Nucleotide Sequence and Expression in Escherichia Coli of the Beta-Cyclodextrin Glycosyltransferase Gene from Bacillus Circulans Strain No. 8
Authors: Nitschke, L. / Heeger, K. / Bender, H. / Schulz, G.E.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 / Non-polymer description / 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_conn_angle / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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_auth_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
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 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)75,7404
Polymers74,5071
Non-polymers1,2333
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.500, 105.000, 113.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLODEXTRIN GLYCOSYLTRANSFERASE / CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE / 1 / 4-ALPHA-D-GLUCAN\:1 / 4-ALPHA-D- ...CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE / 1 / 4-ALPHA-D-GLUCAN\:1 / 4-ALPHA-D-GLUCOPYRANOSYLTRANSFERASE (CYCLIZING)


Mass: 74507.008 Da / Num. of mol.: 1 / Mutation: E257A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 8 / Cellular location: EXTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
References: UniProt: P30920, cyclomaltodextrin glucanotransferase
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %(v/v)protein1drop
27-15 mg/mlCGTase1drop
350 mMtriethanolamine-HCl/sodium-citrate1drop
40.5 %PEG15001drop
550 mMtriethanolamine-HCl/sodium-citrate1reservoir
60.5 %PEG15001reservoir
70.9-1.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→29.24 Å / Num. obs: 42278 / % possible obs: 89.1 % / Redundancy: 4.3 % / Rsym value: 0.096 / Net I/σ(I): 7.2
Reflection shellResolution: 2.41→2.48 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.266 / % possible all: 71.5
Reflection
*PLUS
Num. measured all: 183009 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 71.5 % / Rmerge(I) obs: 0.266

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1255 3 %RANDOM
Rwork0.177 ---
obs0.177 41397 --
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 79 205 5547
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.377 126 3.2 %
Rwork0.288 3794 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION4BCD-TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.288

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