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- PDB-9cgt: STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A TH... -

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Basic information

Entry
Database: PDB / ID: 9cgt
TitleSTRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A THIO-MALTOPENTAOSE
ComponentsPROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / 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
thio-maltopentaose / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsSchmidt, A.K. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Substrate binding to a cyclodextrin glycosyltransferase and mutations increasing the gamma-cyclodextrin production.
Authors: Parsiegla, G. / Schmidt, A.K. / Schulz, G.E.
#1: 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.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Cyclodextrin Glycosyltransferase Refined at 2.0 A Resolution
Authors: Klein, C. / Schulz, G.E.
#4: 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
DepositionSep 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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_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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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 / _struct_asym.entity_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 2.2Oct 30, 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: PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4644
Polymers74,5071
Non-polymers9573
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.600, 104.700, 113.600
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 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 alpha-D-glucopyranose-(1-4)-4-thio-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio- ...alpha-D-glucopyranose-(1-4)-4-thio-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-alpha-D-glucopyranose-(1-4)-1-thio-alpha-D-glucopyranose / thio-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 876.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: thio-maltopentaose
DescriptorTypeProgram
WURCS=2.0/2,5,4/[a2122h-1a_1-5_1*S][a2122h-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1*S*_c4-d1_d4-e1*S*WURCSPDB2Glycan 1.1.0
[][a-D-Glcp1SH]{[(4+1)][a-D-Glcp4SH]{[(4+S)][a-D-Glcp]{[(4+1)][a-D-Glcp4SH]{[(4+S)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#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.: 199 / 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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growpH: 6.9 / Details: pH 6.9

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.218→33.361 Å / Num. obs: 42320 / % possible obs: 75.1 % / Redundancy: 2.2 % / Rsym value: 0.039 / Net I/σ(I): 17
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 1 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.118 / % possible all: 19.3

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1055 3 %RANDOM
Rwork0.147 ---
obs0.147 34739 90 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 58 199 5520
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.252 106 3 %
Rwork0.227 3471 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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